Trigun: Knives, being something of a Psychopathic Manchild, doesn't understand why his twin brother Vash would choose to side with the humans over himself, when the humans (in Knives' eyes) are nothing more than parasites who leech the lives of Plants (from whom Knives and Vash were born).
Giese Hunt assumes that the reason why Johan uses the Crystal Beast cards is because he seeks its ace card, Rainbow Dragon, to sell for profit, which is what Giese seeks it for. Johan angrily retorts that the Crystal Beast cards have a bond with and chose him as their master, and even if he found Rainbow Dragon, he would only treat it as another friend.
Yu-Gi-Oh!: During the Death-T arc, when Yugi and his pals are trapped in the Death T-3 room, which involves giant blocks falling and attempting to crush them, Kaiba firmly believes that everyone only cares about themselves most of all and at least one of Yugi's group will betray the others to save themselves. Honda/Tristan proves him wrong when he is pinned by the jacket between two blocks, helping Yugi escape and remaining behind.
If Shin really knew and loved Yuria, he really shouldn't be surprised that she was Driven to Suicide by the cruelty and genocide committed in the name of earning her love. It's revealed in a later episode (though in chronological order in Yuria Den) that he realized she was lost to him, after she survived her fall only to unconsciously call for Ken.
In the case of Raoh, he's so emotionally stunted by his drive to conquer the world that while he still gets brotherly love (hence one of the anime's most touching scenes), romantic love flies right over his head. As a result, he mistook his relationships with Reina and Yuria for ambition (Reina as a comrade in his ambition, Yuria as the source/prize of his ambition) instead of could-have-been-love. The sheer ignorance of Raoh's response, when he's subsequently frightened both by Kenshiro and by Fudou's children, wondering at the source of Kenshiro's power...
After Jackal's gang murdered an old lady that was taking care of a bunch of little children, Kenshiro swore tracking, finding and killing all of them. Of course, he began to make just that. After finding a corpse of one of his comrades, a bandit said he didn't understand why Kenshiro was doing something he gained nothing with.
In Cyborg 009, 004 was faced with a fully robot duplicate of himself which was not only stronger and faster, but could perfectly predict his actions. Until their battle knocked a bird's nest loose from a tree; the mere act of 004 diving to catch it was so unexpected to the robot that it was effectively a Logic Bomb and caused the robot to malfunction and shut down.
The DarkstalkersOVA had Bishamon suffer this when Donovan put himself at risk to save human bystanders during their fight.
Naraku, from InuYasha, privately expresses some confusion when Sangosimply will not kill her little brother Kohaku, no matter what he makes him do. While he was played for this trope for most of the series, another particarly despicable instance being when he claims the way the protagonists would just show mercy to a loyal underling whom he just sent on a suicide mission to take them out makes him sick, he is ultimately revealed to be an interesting subversion when Kagome points out that he is part human and couldn't possibly carried out his Manipulative Bastard antics if he didn't understand the meaning of human bonds, which, on the one hand, manages to make him a great deal more terrifying as a villain than he would be if he simply didn't get goodness, since it means that he always knew exactly what his actions would do to the protagonists, but on the other hand revealed that his motivations had to go beyond mere lust for power. It is interesting that he was never really aware that the vestiges of humanity he tried so hard to get rid of were, in fact, as much of an asset to him as they were to the protagonist.
Similarly to the example from Black Lagoon, in the manga version of Battle Royale, Mitsuko Souma is captured by Tadakatsu, a baseball player, and Yuichiro, an otaku. While Tadakatsu is wary of her, Yuichiro is more sympathetic and makes the effort to talk to her. Having been abused and exploited by men for most of her life, Mitsuko assumes that Yuichiro's just trying to get into her knickers when he offers to untie her hands. However, she's surprised to discover that he's just going to give her a drink and has no ulterior motives, and is even more surprised when he takes a bullet from Tadakatsu to protect her.
Mello had kidnapped and traumatized Sayu. Soichiro, Sayu and Light's father, had managed to get the Shinigami Eyes and got back the notebook. Light was expecting his father to write out Mello's name as soon as he saw his face but Soichiro simply threatened Mello, preferring to arrest him. Light couldn't understand why Soichiro would do that.
Used again with Mello and Light later on, after Mello kidnaps Takada. Mello is killed in ensuing events. Light, whose first loyalty is to his own survival, cannot conceive that someone like Mello would sacrifice himself for any reason and walks right into the trap convinced that Mello was just an idiot. Although not exactly hero and villain, this is clearly a case of selfishness cannot comprehend loyalty. It's worth noting that with other characters that are more clearly good guys, Light tends to have better success predicting their behavior - Near is an example - but, perhaps because Mello demonstrates a kindred disregard for human life early on, Light simply assumes that the other is driven by greed rather than revenge.
The Antispiral's speech to Nia in the final episode of Tengen Toppa Gurren Lagann would indicate that it doesn't understand why humanity continues to fight against the impossible odds it faces: "Your actions are baffling, Irregular. Why do you resist us so?" Nia then lampshades the trope, stating that the Anti-Spiral cannot possibly understand and that it should stop trying. The Anti-Spiral responds with a strange statement that understanding is not necessary; they only want knowledge.
In Rurouni Kenshin, Kanryu Takeda does not understand why the heroes are trying to rescue Megumi even though there is no reward waiting for them. He is even more bewildered that they refuse to take his bribes.
Black Cat: Creed is the living embodiment of this, although it verges on "Insanity Cannot Comprehend Sanity" at times. Literally every problem in series was triggered by Creed's inability to process, or even understand, ordinary human feelings. Creed honestly can't understand why his murder of Saya would prevent Train from wanting to join him. Similarly, it leaves him unable to understand why his Bad Boss tendencies will lead to poor morale among his subordinates. Creed seems to see people as existing apart from one another and, as such, social cause and effect has almost no meaning for him, which only fuels his issues.
In Yu-Gi-Oh! 5Ds, Jose doesn't understand why Crow would lose on purpose just to give Yusei a fighting chance in their tag-team duel.
As a part of his Villain Decay down to Smug Snake, Bleach's Sosuke Aizen gets hit with this by the end of his character arc. When Ichigo first confronts him, Aizen attempts to mess with his head by claiming Ichigo has no reason to hate him and is only fighting out of duty even though he and Ichigo both know Aizen will murder everyone Ichigo knows and loves if he's not stopped. Later on, when Ichigo reappears, clearly looking like he Took a Level in Badass, Aizen assumes the new form is no threat at all because Ichigo changed in a way he hadn't predicted. It hits Aizen much harder in relation to Urahara, however; Aizen appears to be genuinely bewildered and outraged that Urahara, the only man he considers his intellectual equal, is not only content to sit idle rather than try to control the afterlife, but also opposed to Aizen's attempts to do so.
Ulquiorra is a much straighter example. He outright states that he doesn't understand why Ichigo fights him, even though he's hopelessly outclassed.
Gaara from Naruto, back when he was an Ax-CrazySerial Killer who honestly though his purpose in life was to kill people, didn't understand how Naruto could keep pushing himself so hard in their final fight, hard enough that even when both of them were utterly exhausted, Gaara was flat on his back but Naruto was crawling on his chest to fight him, because that was the only way to save Sakura and his friends. He only quit when Sasuke showed up and told him Sakura was safe. Naruto got Gaara just fine, though; he knew exactly what Gaara had been through and explained to him that it was finding friends like them that saved him from the dark, angry place Gaara was in himself. Worth noting is that Gaara takes this to heart and while he never quite loses the creepy vibe he gives off, he proves to be just as loyal to his friends and family as Naruto himself.
This is the reason that Dark Star merges with his mortal enemy Vorfeed to become an entity to destroy all universes and then rebuild them into a world where the two of them would not need to fight each other anymore.
In the manga, Knight of the Aqua Lord, the Big Bad of that season took the power of a god and went insane.
Tao En/Yuan in Shaman King, who refuses to believe that you can trust anyone due to the way his ancestors were persecuted for their shaman powers. This is crucial to his defeat - he's more powerful than any of the main characters at that point, but watching The Power of Friendship trump self-preservation destroys his focus.
The undeniable Queen of Evil in all Gundam Universes, Katejina Loos from Mobile Suit Victory Gundam, literally got sick since she couldn't comprehend Shakti's thoughts of ending the battle and preserving life.
Haman Khan from Mobile Suit Gundam ZZ descended into cynicism and nihilism well before the series began, which is why she can't understand why Judau refuses to join her. She tries several separate approaches to manipulate and seduce him to her side, but all fail.
This happens to the homunculus Envy in Fullmetal Alchemist. He (well, Envy's genderless) gets baffled and frustrated by how so many former enemies are setting aside their differences and teaming up to defeat Father's forces. He unsuccessfully tries to remind them of how much they should hate each other. When Envy realizes that he envied humans' kindness and decency all along, he takes his own life out of humiliation.
It also happens, to a lesser extent, to Wrath and his minions a bit later. They correctly guessed that they could use Love Is a Weakness against Roy Mustang, by slashing the throat of his beloved aide Riza Hawkeye and using her life as motivation for him to perform the forbidden human transmutation, which they needed in order to turn him into one of their sacrifices. What they didn't bank on was Riza fighting death long enough to urge him to refuse, and on the arrival of The Cavalry to help save her. Wrath even comments on it after the fact, saying that he really hates it when humans behave in a way he doesn't expect.
In the Diamond and Pearl arc this is the reason why Paul could not raise Chimchar to his full potential; as he thought making friends with his Pokémon was a waste of time. This came back to bite him in the ass when Ash raised said Chimchar into an Infernape and beat him in the Pokémon league.
In Best Wishes 2 Episode N's Grand Finale, Colress and Ghetsis are astonished at the fact that Ash's Pikachu and Reshiram freed themselves from the Pokémon Control Machine under their own power, and don't understand how they could. They are so awestruck at how their plans failed that it sends them both into a Villainous Breakdown.
Natsu Tanimoto came across as this after he was first revealed to be Hermit, the Fifth Fist of Ragnarok; he refused to believe that Kenichi's sense of right and justice was anything more than a facade. This was eventually justified by his Freudian Excuse (his adopted father was killed by his wife who pretended to love him just to get close to him for his money, and later Natsu himself was betrayed by an associate of the senior Tanimoto who pretended to be trustworthy just for the chance to off Natsu and get his fortune for himself), but after he realized that Kenichi really did believe in his own ideals, he pulled a sort-of Heel-Face Turn and is currently a Jerk with a Heart of Gold.
In Rosario + Vampire, Kiria gets confused when Kurumu saves her rival-in-love Moka's life. Kurumu angrily explains that just because she's jealous of Moka doesn't mean she hates her or wants her to die.
Minerva of Fairy Tail is so dangerous partially because of how she inverts this. She fully recognizes how some fighters become more dangerous when motivated by The Power of Friendship, and plans to use it to devastating effect with Sting in the Grand Magic Tournament.
When Byro tries to kill Coco for treason, Lucy steps in to defend her. Byro asks why she would care about her, especially since Coco was from the enemy's side. Lucy replies, "I have to care about her, because you don't."
Soul Eater: Spoiler example: In the anime, Asura is defeated because he can't understand why Maka keeps fighting despite being clearly outmatched. His inability to understand the concept of bravery and dedication confuses him, allowing Maka to land a fatal blow.
Stein has a relevant line when witch Medusa confesses her love for him:
Shizuri Mugino gets attacked by an unnamed assailant who uses a Shape Shifter Guilt Trip against her. He says Love Is a Weakness and that her love for Shiage Hamazura and her guilt over killing Frenda Seivelun will weaken her enough for him to crush her. Instead, she massacres him. The assailant is shocked and asks how. Mugino says The Power of Love has made her stronger than ever before, and the assailant is baffled.
Leivinia Birdway can easily enter the mindset of politicians and master schemers like Aleister Crowley to predict their actions and motivations. However, Touma Kamijou'sdrive to help and protect others without expecting any reward or having any ulterior motives makes absolutely no sense to her. She eventually concludes that he is insane.
The Big Bad of the second arc of Sword Art Online thinks that Kirito will be too afraid to even enter the game to save his kidnapped wife, and gloats about this to said wife in order to demoralize her. Not only is Kirito more than strong enough to dive headfirst into the game on the off chance he can save Asuna, she is well aware of that, and hearing that Kirito knows she's in danger is enough to keep her going for a little while longer.
In one of the earliest stories told with the Corrupt Corporate Executive version of Lex Luthor (in Superman vol. 2 #2, 1987), Luthor notices that Clark Kent has some kind of connection with Superman and sets up a research project to find out the nature of the connection. When the researcher concludes that Clark Kent is Superman, Luthor fires her and scraps the project... because, to Luthor, it's impossible to believe that someone with that much power would want to waste time occupying such a humble persona. It comes around full circle in Action Comics vol. 1 #900. After achieving godhood, Luthor starts torturing Superman, thinking that he only simulates emotions. When Superman provokes Luthor to delve deeper and watches Jonathan Kent's death, Luthor puts two and two together and promptly has a Villainous Breakdown because he can't understand how someone like Superman could have a loving family like the Kents and Luthor didn't.
In the original Silver Age "Death of Superman" story, Luthor sits smugly through the Kandorians' trial, confident that he can bribe his way out. When asked for his plea, he answers that he is guilty. However, if they let him go, he will work out a way to restore them to full size. Luthor is taken aback when the judge retorts that "we of Kandor do not make deals with murderers" and orders him sent to the Phantom Zone for all eternity.
At the end of "Superman's Phantom Pal", Superman explains to the villainous inhabitants of the Phantom Zone that Jimmy didn't give in to the temptation to spy on his secret identity because of the boy's "loyalty and honor." He then finishes up his speech by invoking this trope.
In All-Star Superman, when Luthor gains Superman's powers, when looking through Superman's eyes and how the Universe is interconnected, he realizes why Superman was so benevolent. So much so he completely atones and accepts his death penalty.
In Archie Comics' Sonic the Hedgehog, Dr. Finitevus turned Knuckles into an insane and ultrapowerful villain and, as a security feature, made sure that the change couldn't be reversed without someone dying for it. That should do it, right? When he explained this, there was silence... for about a second, at which point everyone present started volunteering. Then the next time Finitevus ran into Knuckles, he honestly seemed surprised when Knuckles refused his offer of alliance; it didn't seem to occur to the "good" doctor that Knuckles would hold a grudge over the brainwashing and the death of his father (who performed the above mentioned Heroic Sacrifice).
The Wizard, long-time foe of the Justice Society of America, had this as his motive in his first appearance. He'd missed the early years of the team as he was in isolation, learning black magic, and when he returned to civilization, the Wizard could not believe that smart people with superpowers would use them for altruistic purposes. Therefore, the JSA had to be pulling the biggest scam ever, and the Wizard demanded to be cut in.
At one point when the Crime Syndicate of Amerika infiltrate the universe of the Justice League, Johnny Quick and Power Ring change costumes and pose as their heroic versions (The Flash and Green Lantern respectively). Almost losing a fight to supervillains, they are absolutely bewildered when civilians rush in with clubs to help them. When asked why they did this, the civilians said that they owed them for all the times the League's helped them. This prompts Power Ring to complain:
Some demons trap Traci 13 in a Lotus-Eater Machine where she is the uncontested ruler of the world and her father is dead. They are baffled when she rejects the illusion and wants her father back. She thought her father was annoying with his uptight refusal to believe in magic, so the demons assumed she would be happy with him gone.
In the DCcrossover eventUnderworld Unleashed, this ends up costing Neron badly when he reveals that his stream of deals with various DC villains and heroes was done solely to get Captain Marvel to cut a deal with him. Unfortunately, Neron thought that the Big Red Cheese would ask for something selfish. Instead, Cap asked for something completely selfless ("Let everyone else go and I'm yours."), which meant that when Neron tried to take Cap's soul, it burned him so badly that he fled. Neron gets similarly burned when he buys the love between The Flash and Linda Park. It causes him to start developing feelings for the souls in his possession, and he doesn't understand why. He ends up giving it up in disgust.
During the John Rogers run of Blue Beetle, Eclipso hits Jaime with a spell that will bring out his "deepest desires", which it believes will be some sort of dark, violent power fantasy. What Eclipso gets instead is... a dentist, as what Jaime really wants is a career that will make enough money to provide for his family.
Joker: It's all a joke! Everything anybody ever valued or struggled for... it's all a monstrous, demented gag! So why can't you see the funny side? (Joker stops smiling) Why aren't you laughing? Batman: (bursts in through a wall) Because I've heard it before... and it wasn't funny the first time.
In volume 2 of Empowered, Emp saves a thug's life by warning him about his impending brain aneurysm and getting him to the hospital in time for an operation. However, on her way out, a pair of nurses drag her into a closet and drug her, complaining that she's ruined the evil scheme they're running from the hospital. The two of them are convinced that Emp's presence means the Superhomies are onto them, since there's no way a superhero would care about the life of a common thug. However, in this case, it's less because they can't understand kindness, and more because most superheroes in this series are assholes.
In Star Wars: Legacy, Darth Krayt's attempts to convert Cade Skywalker into a Sith fail because Cade doesn't want the power Krayt is offering him. Keep in mind that at this point Cade is still rejecting the Jedi calling — he just doesn't want power. The idea that someone might not want power is something utterly alien to the Sith, who all more or less became Sith because they wanted power.
In Forever Evil the Crime Syndicate is perplexed by the idea of justice.
In Superman: Brainiac, Brainiac has stolen the city of Metropolis for his collection and is deriding Earth's perceived flaws to the captive Superman; it has none of Krypton's science, its' weapons are primitive. He concludes that the entire culture is useless and asks Superman what they could possibly offer him. The whole time he's talking, Lois Lane, thinking the end is nigh, is desperately crying out to Superman from the shrunken Metropolis, trying to tell him she loves him before it's too late. The implication is that if Brainiac had listened to her, he would have the answer to his question.
Both averted and played straight in Grant Morrison's "JLA: Earth 2" graphic novel. In an alternate universe where evil always wins and good always fails, the Justice League realize that the only way to defeat Brainiac is by walking away in the middle of the crisis. Played straight in the way Brainiac really didn't expect them to do it, and is punished harshly when the 'evil' Justice League return home.
Ikazuki subtly shows he has a shade of this as well: he shows open disdain for human nobility, and can't seem to understand why Tohru still cares for Jade.
Drago has this as well, as Karasu points out in their fight. Because Shendu was sucha horrible father to Drago, the young dragon views offspring as an investment, and is unable to understand why the Matriarch chose Karasu, an elite warrior, to watch her daughter, and why Jade (AKA the Matriarch) cares about the ones she loves.
In Kage (a Project Dark Jade fic, just like Queen Of All Oni above), Miranda is completely baffled when Tracker lets Jade get nice with Sniffer after Jade gave the hound some of her food. Since she considers Tracker to be an even bigger monster than herself, she can't believe he would be civil with Jade simply because of that, and the only way she can explain it to herself is by assuming that Jade used some kind of spell. She's still convinced Jade is using magic when the spider-girl sees her playing with Tracker a couple chapters later.
Getting Back on Your Hooves' Big Bad, Checker Monarch (Trixie's sister), has this problem — specifically, she's so far miscalculated how much Trixie's friends care about her and how willing they are to forgive her. Justified as, according to Word of God, she's based on real life sociopaths, who, by definition, are unable to understand concepts such as compassion and empathy.
In the sequel Tarnished Diamonds, after the previous story's Big Bad, Checker Monarch, told Diamond Tiara she was just like her as a filly, then had her schemes exposed, Diamond is trying to change, not wanting to turn out like Checker, especially since she loves her family and doesn't want to become someone who would torture them. The thing is, while she's had a Heel Realization, she doesn't yet get why bullying the CMC is wrong (though she is trying to repress her desire to do so).
Discord has this problem, and it's even outright mentioned at one point by Twilight as being his Fatal Flaw. Celestia also mentions in the Origins Arc that Discord was completely incapable of truly comprehending love and is the only one of his family who had this problem, including his two Eldritch Abomination parents, Havoc and Entropy. Notably, Word of God confirmed that Entropy, despite being an Omnicidal Maniac by job description, comprehended it, and yet Discord can't. Discord knows this himself, but has simply chosen to ignore it and continue his sick games.
Discord is such an extreme example of this that even his own acts of compassion baffle him. In the Epilogue timeline, Equestria is invaded by aliens. Discord travels to the heart of the alien empire to prank their leader...and discovers a dying and sick old man on life support. Discord is filled with pity at the sight and gives the old man a day of perfect health. When Discord returns home he goes on a tirade because he doesn't understand why he felt so sorry for the man.
Dark World offers another example in the Valeyard, who views working with others as a weakness and fails to understand why the heroes won't give up fighting. The former leads to his defeat, as it's the heroes working together that brings about his defeat.
The Immortal Game is notable in that every single villain in the story has this problem, to varying degrees. The only one who is close to understanding how the heroes think is Nihilus, who has access to all of Twilight's memories, and even she underestimates them in the end.
In The Last Son, Magneto, Doctor Doom, Sebastian Shaw, General Zod, and Apocalypse cannot understand why Superman does not use his powers to conquer the world.
Darkseid, as usual. It comes with the territory of being the God of Evil and all.
In Return to Prince Manor the son of the Queen of the Winter Court assumed mental control over Harry and Draco and commanded them to kill Snape. Problem was:
Jarillion might be a master of compulsion, and his love of discord second to none, but one thing he had never understood — and that was how the ties of blood and love bound one another, a love so powerful that even the best spell of obedience could not compel Harry to destroy Severus.
In the Chaos Verse (a spin off of the Pony POV Series), the Big Bad is shown to suffer from this: Nightmare Phobia is able to manipulate and feed off of ponies' fears, but she doesn't understand how they're able to fight those fears and break free of her control.
In Children of Time, this trope is Averted, Defied, and Discussed. This is what makes Professor Moriarty an even more dangerous opponent than he was in the Sherlockian Canon — he even goes so far as to mock Holmes for not having studied the affairs of the heart.
In "Metamorphosis," a part of the MLP fanfic series The Nuptialverse, Queen Chrysalis is shown to not understand why Twilight still fought for her mentor, her brother, and her friends, even after they outright abandoned her, or how Cadence could continue to love a stallion that let her down.
Olive Branch, the Big Bad of Families, refuses to believe that anyone as powerful as the Princesses is as selfless as they appear.
A minor example, but Olive Branch also cannot fathom why most citizens still support Princess Celestia despite letting the Changeling Invasion happen.
A flashback to Sunset Shimmer's foalhood reveals that Celestia had her look into a magic mirror that shows the viewer their deepest desires. For Sunset, it was becoming an Alicorn and ruling solely over Equestria, and she seemed rather confused when this unsettled Celestia.
Celestia discusses this trope with Fluttershy in Direction and explains it to her — truly evil beings deny seeing anything good in the world, because they are unable to grasp that others aren't as self-centered as they are.
Wesker in My Little Wesker can't understand why these ponies act so friendly and trusting to everyone they meet, after he's stuck there as a pony. At first, he's paranoid that it's all an act to gain his trust, but then concludes that these ponies are too stupid for malice.
During the final fight of the first arc, General Zod expresses confusion as to why Rainbow Dash/Supermare would settle for being Equestria's hero, when as a Kryptonian she could rule as a god.
In the second arc, Brainiac is a being that runs completely on logic, and is thus thrown for a loop when Rainbow Dash takes a third option, based entirely on emotion, to escape a Sadistic Choice that, logically, should have been escape proof.
In The Princess of Themyscria, Ares seems absolutely baffled when Diana decides to keep fighting him to protect the mortal realm from his attempts at a Forever War, when he can't see anything of worth to protect.
In the Danny Phantom and Teen Titans fanfic called "Haunted Destiny", the evil ghost Valara fails to understand why Danny won't return her love after deciding to kill off innocent people to make him have more time for her.
Gaston is unable to imagine why Belle would choose the Beast over him. To him, love is just a convenient bargaining chip — or a distraction, or a function of physical beauty.
Gaston is seemingly unable to understand why the Beast let him live at the end, if his final attack is any indication.
When the Beast is still selfish at the beginning of the film, he seems genuinely shocked that Belle would give up her freedom to take her father's place as a prisoner.
Kung Fu Panda 2. Instead of questioning how Po was able to grab the cannonballs and throw them back at his ships, Shen is baffled how Po was able to attain inner peace despite facing the one who murdered his birth parents and wiped out his people. For years, Shen has allowed the day his parents banished him to be the thing that drives him to get what he wants and continuously ignores the Soothsayer's requests that he not let his past control him. The fact that Po attained what Shen had wanted for years, inner peace, by listening to the same advice Shen ignored, completely baffles him.
While they're more 'weird' than 'evil', this is the basic premise of The Nightmare Before Christmas. Jack understands the basic feeling behind Christmas, but not how traditional Christmas icons translate into Christmas feelings. The other townsfolk don't have a clue and merrily set about to twisting Christmas toys to their own scary designs because they feel this improves them.
In Disney's Sleeping Beauty, the Good Fairies disguise themselves as human peasants, give up their magic, move into a cottage in the forest, and raise Aurora/Briar Rose as though she were a foundling, because they know it will never cross Maleficent's mind that anyone could perform such a selfless act. As Fauna notes: "Maleficent doesn't know anything about love, or kindness, or the joy of helping others. You know, sometimes I don't think she's really very happy."
In Cinderella III: A Twist in Time, Lady Tremaine and Drizella don't believe in love and think that the Prince and the King are only nice to them because they are obligated to be. In contrast, Anastasia picks up on the fact that The Power of Love is more powerful than magic and that the Prince and the King are genuinely nice people. She quickly does a Heel-Face Turn.
Film — Live Action
The Tag Line to Pan's Labyrinth is "Innocence has a power evil cannot comprehend", which explains a lot of Cpt. Vidal's actions, as well as his inability to see the Faun at the end.
Emperor Palpatine's arrogance and relentless self-centeredness blind him to the idea that Luke would show mercy and redeem his father instead of co-ruling the Galaxy — with someone he is destined to overthrow in due time, no less — causing his carefully-laid plans to fail. The idea that Darth Vader would turn on him rather than watch his son be murdered presumably never entered his mind either.
This is foreshadowed earlier, when Vader senses Luke aboard a captured Imperial shuttle headed for Endor. Palpatine comments that he cannot sense anything - presumably because he's turned so completely to the Dark Side that he simply doesn't recognize the rest of the Force. It also explains why he isn't more careful about provoking Vader's Heel-Face Turn: he could only sense the evil side of him.
For Luke specifically, his main error was in not realizing that Luke didn't really seek power, to the point that some in the expanded universe speculate on whether he even really understood the idea of wanting it. While rage against Vader and the Emperor was a temptation to the Dark Side, he really had no reason to side with them.
The Joker's "social experiment" uses The Sadistic Choice in an attempt to prove that people are cruel at heart, but both groups do the right thing. In a gloriously believable way, no less. It's not a stretch to think that not a single typical civilian will be cruel and cold enough to actually blow up a ship, even one full of criminals. Flip side, it's also believable that there might be just one guy on the ship of criminals who's not all bad. Batman even spells this trope out to the Joker, who can only look at the ships, dumbfounded and disappointed.
Batman: What were you hoping to prove? That, deep down, everyone's as ugly as you? You're alone!
What makes it even more this trope is that the Joker wasn't counting on a convict having turned his life around.
In Schindler's List, Amon Goeth often can't understand Schindler's actions of compassion towards his Jewish workers. In particular, he acts thoroughly confused when Oskar wants to buy all of them before they go to Auschwitz, trying to figure out how Oskar will make money off this. It never once occurs to him that Oskar might simply want to save a thousand people from genocide.
Occurs again in the third film. Sentinel Prime has decided to cooperate with the Decepticons to enslave humanity as a work force to rebuild Cybertron. He makes it clear that he wants to ensure that the Cybertronian race doesn't die out and believes his authority as a Prime puts him above coexisting peacefully with humans. So it becomes a huge case of frustration for him when Optimus Prime, his former student, chooses to defend the freedom of mankind over the possibility of having his home restored. Optimus simply responds by saying that it was Sentinel who taught him that "freedom was everyone's right."
In Patton, one German points out that Patton, who they believe will lead the invasion of Europe, is facing a public backlash after slapping a soldier and may be court-martialed. He gets the reply "Don't believe their newspapers! They would never keep their best general out of the war just for slapping a soldier." Of course, that's exactly what they do (albeit as part of a Batman Gambit). This is an interesting case, as in the harsh reality of war, overlooking personal failings — even major personal crimes — of a great general might really be the "good" thing to do, not just the expedient thing. Keeping your best leaders in the field saves soldier's lives. note And you can always punish him after he's done doing his job, after all. Patton's commander, Eisenhower, thought the man was Ax-Crazy and liable to screw up the Alliance with his rivalry with Montgomery and his open hostility towards the Soviet Union. Putting him in charge of the decoy invasion served two purposes for Ike: it convinced the Germans that the decoy was actually real, and it kept Patton out of the front lines (and the headlines).
In The Magnificent Seven, Callvera's last words to Chris were "You came back. Why?" The reason he let them go in the first place was because he thought they were all on the same terms, and thus they would never come back to save a bunch of farmers.
Played straight in The Matrix Revolutions - Neo's refusal to give up, no matter how badly he's beaten, allows him to push Smith into a Villainous Breakdown without saying a word. Then Neo allows Smith to assimilate him. Smith is completely surprised that Neo would do such a thing, and is even more surprised when, his purpose fulfilled, he is wiped out of existence.
Mr. Potter from It's a Wonderful Life goes through the entire movie without picking up so much as a clue as to what makes Peter, George, or indeed any of the Bedford Falls townspeople tick. Potter's expectations that George will hand the Building and Loan over to him in exchange for a job or that the townspeople will quickly turn against George at the first opportunity are disappointed throughout the movie. It never dawns on him there's something about his fellow men that he just doesn't get.
In Superman II, General Zod and Ursa assume Supes is protecting the humans because they are his pets.
In the end, the Big Bad of Ghost Ship tries to tempt the Final Girl into his trap by turning into the crew mate that he just killed. He attempts to use the crewman's love to trick her, but fails horribly because he believes the material items he offers will win her over. Shows up after his ruse is uncovered when he tries to trade her life for keeping the ship afloat and can't seem to understand that she doesn't care that she may die if she can destroy the ship and free all the trapped souls.
In Prince of Persia: The Sands of Time, while beating him up, Nizam remarks to Dastan his dislike of the King adopting the homeless boy and making him Prince. Earlier, the King did explain that Dastan is brave and noble, so he judged him worthy of becoming Prince.
Nizam: I never understood why my brother brought trash into our house! Enjoy the gutter, Dastan! It's where you will stay under my rule!
In Sherlock Holmes, both Holmes and Moriarty employ a Sherlock Scan to predict the outcome of their final confrontation, and both come to the same conclusion: that due to Holmes' injured shoulder, he can't win. However, Moriarty - self-interested to the point of outright sociopathy - couldn't comprehend that Holmes was willing to sacrifice his own life to defeat him.
In Daredevil, after the titular superhero has soundly defeated the Kingpin and has a chance to Finish Him!, Kingpin is dumbfounded by Daredevil's refusal to do so.
Oh, God! You Devil features George Burns as both God and the Devil. When the Devil has manipulated a man into attempting suicide, he and God have a poker showdown for the soul. God raises the stakes, offering to cease protecting a great many of people at risk if he loses, but that the Devil will cease interfering if God wins. When the Devil considers the offer, he decides there's no way God would do this without being certain of victory, since one man wasn't worth it. To Him, one man was. It's played for a strange form of PG-rated Black Comedy.
In The Last Samurai, Nathan Algren is greatly haunted by the atrocities he committed in the past as a soldier. His fellow soldier Bagley sees his own atrocities as duty and barely remembers them. Bagley cannot understand why Algren is so bothered by them.
In Little Shop of Horrors, Orin Scrivello, D.D.S., doesn't understand why Seymour Krelborn would want to kill him, because Scrivello had never done anything to Seymour. He never imagines that anyone would want to protect Audrey, of all people.
Orin Scrivello, D.D.S.: "What did I ever do to you?"
Seymour Krelborn: "Nothing. It's what you did to her."
Orin Scrivello, D.D.S.: "Her who?"
Seymour Krelborn: "..."
Orin Scrivello, D.D.S.: "Oh. Her."
In Mistborn, this is Ruin's undoing. He is sentient destruction and entropy, and only builds up one thing if he knows he can use it to destroy two or more other things later. He is literally incapable of understanding human love and emotion, that there is more to life than the chaos of death at the end, why anyone would create something and NOT seek to destroy it later, but see it grow instead. Thus, when his unwilling servant kills Elend, Vin no longer has a reason NOT to sacrifice herself, and uses the power she inherited from Preservation (Ruin's counterpart that gave up a piece of his soul to give mankind sentience), to destroy him, (which Preservation was literally incapable of doing, so he created humanity to do so for him).
The plan to throw the Ring into Mount Doom in J.R.R. Tolkien's The Lord of the Rings is largely this trope played straight, but with a subversion at the end. Gandalf's plan hinges on the trope: "Well, let folly be our cloak, a veil before the eyes of the Enemy... the only measure that he knows is desire, desire for power; and so he judges all hearts. Into his heart the thought will not enter that any will refuse it, that having the Ring we may seek to destroy it." This assessment proves correct, and Gandalf and Aragorn are thus able to bluff Sauron into concentrating his attention on Gondor, allowing Frodo and Sam to slip into Mordor undetected. And, indeed, the moment Frodo puts on the ring inside Mount Doom, making its location known, Sauron immediately realizes the depth of his own folly and how close his destruction is. However, it turns out that Sauron is also correct — when the moment of truth comes, it is revealed that no-one can actually muster the will to destroy the Ring. Only Frodo's (and Sam's) earlier display of mercy to Gollum prevents Sauron's triumph.
Then again, Sauron's belief wasn't that no one would succeed in the end, but that no one would even think of trying. To have the greatest weapon in the entire world in your hands, and give it up — even consider giving it up? Unthinkable.
In the Silmarillion, Morgoth never expects the Valar to come to the aid of the Noldor because "for him that is pitiless, the deeds of pity are ever strange and beyond reckoning."
In David Edding's Tamuli trilogy, it is revealed that the Evil Plan of the guy who was behind the scenes in the The Elenium trilogy went belly up when one person did something he couldn't imagine happening: she gave the MacGuffin with ultimate power to someone else instead of keeping it herself.
Animorphs: At the end of VISSER it's revealed that Visser One cannot understand the concept of love, in spite of having lived among humans for years and even going so far as to bear children and have a family.
Caine Soren from the GONE series seems genuinely puzzled in LIES as to why his female counterpart Diana Ladris doesn't want him to throw a helicopter full of children into a cliff.
Harry Potter: It is repeatedly and explicitly stated that his inability to feel anything for anyone other than himself is Voldemort's Fatal Flaw.
In the first book, Quirrell sums up Voldemort's philosophy with the line "There is no good and evil; there is only power and those too weak to seek it." The line is said by Voldemort himself in the movie.
In the fifth book, Dumbledore and Snape suspect Voldemort has discovered Harry's ability to access his mind, and that he might attempt to do the same, or worse, possess him entirely. At the climax, Voldemort succeeds and Harry begs to be killed, but the thought of seeing his dead godfather again hurts Voldemort so much that his possession of Harry breaks.
It's his inability to understand the meaning of "master of death" that stumps him. Voldemort considers it immortality because he cannot see the world beyond himself. Harry demonstrates that it is actually walking into death without fear. Ironically enough, this course of action ends with Harry's resurrection and Voldemort's Karmic Death.
Voldemort also plays with this by challenging Harry to turn himself in, claiming that he will spare the other students of Hogwarts (or the pure-bloods, at least) if he does so. As Harry eavesdrops on Voldemort, Voldemort comments that he was honestly expecting it to work. However, at the same time, Harry points out that with this move, Voldemort made the exact same mistake again as he did the night he killed his parents: forgetting the power inherent in a Heroic Sacrifice. Inherent in the challenge is the fact that he assumes Harry is using everyone around him as armor. It is incomprehensible to him that Harry's friends are fighting and dying of their own free will to protect someone else. Voldemort may understand intellectually that he can get what he wants from someone by threatening those they care for, but he doesn't understand why they behave this way.
Two of Voldemort's followers betray him out of love for another — Snape secretly switched sides because Voldemort killed Lily, and Narcissa Malfoy withheld key information from Voldemort to protect her son.
As the Villain Protagonist himself notes, an inherent problem demons have in their battle against God is that they fundamentally don't understand His motivation; the denizens of Hell believe that the whole concept of "love" is a cover story for something more selfish and nefarious. Hell even has a division of their research department dedicated to comprehending good. It's one of the worse jobs to get in Hell.
Further on in the book, Lewis seems to suggest that this problem is rooted in the nature of what evil is, in that evil is fundamentally incapable of creatively existing without good.
"He has filled His world full of pleasures. There are things for humans to do all day long without His minding in the least — sleeping, washing, eating, drinking, making love, playing, praying, working. Everything has to be twisted before it's any use to us. We fight under cruel disadvantages. Nothing is naturally on our side."
In The Lion, the Witch, and the Wardrobe, Jadis mocks Aslan for letting her kill him in Edmund's place. Just before she stabs him, she laughs about how it's a pointless sacrifice, as she'll just kill Edmund in the battle the next day. Aslan even tells this to Susan and Lucy, that the only reason the Witch didn't realize what would happen was because she didn't understand the true meaning of "sacrifice".
Lewis asserts this straightforwardly, in his own voice, in Mere Christianity: "Good people know about both good and evil: bad people do not know about either."
While not evil necessarily (more like inhuman), Vlad notes this about the Jeonine in the Dragaera book Issola. They hire him to kill the goddess Vera (who he's rather pissed off at), and he comments to his friends how they obviously have no understanding at all of humanity, to think he would actually do this.
Good has trouble comprehending evil in the Discworld novel Wyrd Sisters. Granny Weatherwax, who will later (Maskerade) explain that if you know the difference between good and evil, you can't choose evil, collapses all the barriers in the Duchess' mind, making her see herself as she really is. After a moment of uncertainty, the Duchess announces "I did it because I enjoyed it, and I'd do it again only hotter and longer! You really believe everyone is good deep down, don't you?" before Nanny Ogg wallops her with a cauldron.
In another Discworld example, the New Death from Reaper Man is absolutely baffled that Miss Flitworth was willing to share her lifetimer's sand with Bill Door, the previous (and good guy) Grim Reaper.
In S.M. Stirling's Island in the Sea of Time series, the otherwise smart and highly competent villain, William Walker, is caught out whenever somebody sacrifices their life to oppose him. He can't comprehend the act, or that being utterly callous and self-serving really offends people who can see through his charm. The scary subversion comes later when after surviving his defeat he never fails to try to understand the motivations and capacities of others.
In Les Misérables, Knight Templar Javert cannot understand why Jean Valjean, someone he views as a criminal and therefore evil, would save his life with nothing to gain. Javert jumps off a bridge so as not to have to perform an evil act himself: either turning in the man who saved him or allowing a criminal to go free.
In A Spell for Chameleon, Trent hands over his sword to Bink so he will be armed while he keeps watch and goes to sleep. Bink and Chameleon reason that Trent, despite the title "Evil Magician Trent", must be trustworthy because he is willing to trust them; an untrustworthy man would not have believed someone else to be trustworthy. (It's not the only evidence in his favor, but it's a strong piece of it.)
In Sandy Mitchell's Ciaphas Cain novel Duty Calls, a renegade Inquisitor is quite certain that Cain will appreciate why he acted as he did. Given that this included staging a massacre, abandoning innocents (including children) to an alien attack, summoning an alien attack to hide his tracks, and no less than three attempts to assassinate Cain, this does not work as expected; even a self-professed Dirty Coward like Cain is horrified.
In Sandy Mitchell's Warhammer 40,000 novel Scourge the Heretic, while Kyrlock and Elyra are infiltrating a smuggling operation, a man goes to rape a girl also waiting to be smuggled. Elyra objects, and not comprehending why, he offers to share. Kyrlock realizes this, says that Elyra wouldn't take him up on it, but he would — which the man cannot believe would be false, so lets Kyrlock get close enough to brain him.
This is actually how the Big Bad in the first Grey Knights book is defeated. His end appearance features him giving a long "The Reason You Suck" Speech, stating that humanity has given up all the morals it previously held dear. He is ironically defeated by one which no daemon has ever understood: willing self sacrifice. With a brilliant Interrogator giving up her life, sanity, and soul in order to learn the daemon's true name so it can be banished.
In Mercedes Lackey's novel The Fairy Godmother, Prince Alexander is hunting when he comes across a knight preparing to rape a peasant girl, and the knight offers to share her with Alexander. Alexander is less than pleased. It's an Elven illusion and the final test of Alexander's redemption.
In the Star Wars: Revenge of the Sith novelisation, Count Dooku is revealed to be incapable of comprehending things like joy and friendship, translating them into things like jealousy, pride, spite, and so forth. Kind of a subversion, because Anakin eventually kills him by calling on something he does understand — RAGE.
The Tarkin Doctrine in the is basically the idea that "Fear of force > force itself", but in practice tends to run towards "Fear is the ultimate weapon", as embodied by deliberately oversized ships, especially the Death Stars. Both sides of this equation fail miserably — the moon-sized Death Stars get blown up by ships less than 35 meters long (an X-wing and the Millennium Falcon), and the main thing about heroism is that it tends to involve courage, the refusal to give in to fear. Essentially, the Tarkin Doctrine is a refusal to understand your opponents turned into a tactical philosophy, with all the success you'd expect.
Almost all of the weapons created following the Tarkin Doctrine meet the same fate, to the point where its lampshaded by Han Solo during the Yuuzan Vong war.
This trope is also essentially what caused Darth Bane's Rule of Two to fall apart, culminating in both Vader's redemption and the events after Caedus' death. Darth Bane created it with the full expectation of the Sith Master either killing the Apprentice if the apprentice fails him or does not have any usefulness left, or otherwise the apprentice offing his master when the opportunity presents itself and/or becoming strong enough to overpower the master. He obviously never anticipated that either of the two would actually redeem themselves to the light side of the force and either abandon the Sith way or also sacrifice themselves to take down the Sith before they killed their loved ones. He really should have anticipated this, since the Sith Lord whose holocron inspired him to create the Rule of Two in the first place, Darth Revan, ultimately renounced the Dark Side, and Bane knew this.
In Luke Skywalker and the Shadows of Mindor, the Big Badthinks he understands, and at least is aware of them, but he vastly underestimates their power. Throughout the book, he goes on at length about how his particular flavor of The Dark Side is greater than any other aspect of The Force. When he puts Leia through a particularly horrible And I Must Scream until her defense breaks, the love she has for Han, even then, hurts him, and he's unable to get through it. In the final confrontation, a Mind Screw-y sequence involving him being the ultimate black hole, he swallows Luke and angrily thinks that if any of the Jedi had ever even glimpsed the truth of the Dark, it would have snuffed their tiny minds like candles in a hurricane-
Was my tiny mind snuffed? I must have missed that part.
Works against the heroes in 'Dead Beat''. Harry says that Butters doesn't know anything, but then risks his life to save him. Thomas points out that the villain won't believe he would do that out of friendship.
In Grave Peril, however, Harry deduces from the attack on Charity and the baby that the Nightmare is being manipulated. As a demon, it couldn't figure out that Revenge by Proxy would be the worst kind of revenge on Michael. He turns out to be only HALF right about this: The Nightmare IS being manipulated, however, it is NOT a demon, but the ghost of a sorcerer that Michael and Harry took out a while back, which would be fully capable of understanding what Michael's family means to him. So this trope ends up being invoked, but not played straight.
Another Dead Beat example. Lasciel simply cannot understand why Harry wouldn't want to be like Nicodemus.
Explicitly pointed out when the Vord Queen is caught by surprise because she couldn't comprehend that the surviving humans (and Marat) would be willing to sacrifice their lives just to have the chance of getting at her, knowing the threat she represented if she survived.
In the next book, Cursor's Fury, the principled Amara and the ruthlessly pragmatic Invidia Aquitane are interrogating a captured spy named Rook who is working for the traitorous High Lord Kalarus. Amara manages to figure out the source of Rook's apparent loyalty to him: Kalarus is holding her daughter hostage to ensure compliance. Once Amara realizes this, she does the last thing either Rook or Invidia expects: she offers to rescue Rook's daughter, because it is the right thing to do. Rook immediately breaks down in tears of relief, while Invidia stares at the whole thing, seemingly unable to comprehend what happened because it doesn't fit into her ruthless and calculated mindset.
Used twice in the fourth book, Captain's Fury. High Lord Kalarus is explicitly said to be ignorant of anything that isn't himself, while Senator Arnos firmly believes that Tavi is an opportunistic politico like himself who only pretends to be The Good Captain for PR reasons, when he's actually the genuine article.
This is something of a theme in the series. In the final book, the Vord Queen devotes much of her effort to comprehending good (or at least, humanity) but largely fails, possibly because the aforementioned Invidia is her "teacher". She learns just enough to get a legitimately moving Alas, Poor Villain moment at the end, though.
Inverted in Eugene Field's Daniel and the Devil: ordinary decent businessman Daniel simply cannot comprehend the Devil's sly temptations and doesn't see the appeal of a life of fun and debauchery, being a respectable businessman and father of nine. This leads to this also being played straight, as the Devil is so flabbergasted by this that he eventually breaks his bond with Daniel, effectively releasing him from his contract AND letting 1001 souls go free from Hell.
In L. Jagi Lamplighter's Prospero In Hell, the reason offered for why the devils tried to frame Cornelius instead of one of her other brothers, which Miranda might have believed.
In Salute the Dark, the Dragonflies are honor bound not to try to reclaim their lands. Stenwold points out that if they gather their armies as if they intended to reclaim them, the Wasps will assume they are not thus bound.
In Aaron Dembski-Bowden's Night Lords novel Soul Hunter, at the end, when Ruven is pondering how to seize power, Talos seizes the chance for Revenge for his murder — of a mere mortal, Talos's servant. To humiliate him, he explicitly says he looks, dying, as that servant's death had looked.
In Death: This trope is used many times. Then again, a number of the villains can be placed in the category of The Sociopath. This causes them to make mistakes that lead to getting arrested or killed off.
The Sword of Truth holds that the truth is objective and self-evident and anyone who doesn't understand is selfish, weak, or deluded. Most of the eleven books are spent foiling, saving, or converting those people, respectively.
According to Jagang, Richard is evil because he's evil.
An entire book is spent with Nicci holding Richard captive, trying to understand him.
Dealing with the people of Anderith is somewhere between this and Refuge in Audacity. You just have to act bigger than them, because they just don't understand compassion.
The Hakens are taught that this is true and that they're evil because their ancestors did evil, and that the Anders are good because they were victimized. It mixes with the most horrifying case of mass stockholm syndrome ever on the Hakens' part.
In the finale, Richard decides that this is true of the Imperial Order because they don't want to understand.
Notably averted with Darken Rahl and the Sisters of the Dark. They understand how good people think and plan on it. Mixes with shades of Dangerously Genre Savvy
Notably averted with the D'Harans, especially the Mord-Sith; it's assumed that this is true, but as Richard, Kahlan, and Zedd get to know some D'Harans and the D'Harans get to know their new Lord Rahl, it turns out that most of the evil of the D'Harans was a reflection of their leader, and that most of them are just people. Not all, though.
In Warrior Cats, Hawkfrost's plan to take over the Clans fails because he literally cannot understand why his brother would earn the position of Clan Leader rather than killing the current leader and taking it.
Overseer Biron, a recurring villain in the Starfleet Corps of Engineers stories, doesn't understand the Federation or its Starfleet heroes, in particular their compassion. Why Starfleet officers and captains expend valuable resources helping non-essential crewmen or those of lesser station is beyond his comprehension. Biron is a highly intelligent being, but a product of a brutal and calculating culture that assigns worth to people based only on how productive and useful they are.
In Sarah A. Hoyt's Darkship Thieves, Thena's father. When he has captured both Kit and Thena, it does not occur to him that Kit has hostage value until she threatens to kill herself if he harms Kit.
In Seanan McGuire's October Daye novel Ashes Of Honor, Samson derides Toby as a sentimental fool and sneers at Tybalt for involving himself with someone so weak.
Myth Adventures: It's selfishness rather than evil, but in Myth-ing Persons Skeeve tries to convince a woman he's attracted to that she doesn't need to stick with her con-artist partner now that he's out of trouble. She has no idea what he means; being in trouble is a reason she'd leave someone, not a reason she'd stick with them.
Various bad guys in the Honor Harrington universe consistently don't realize that sometimes Good Is Not Nice when dealing with Manticore and its allies, summed up rather neatly when Aivars Terekhov, coming to the rescue of the people rebelling against a planetary dictatorship, informs them of this fact.
Terekhov: "Why is it that people like you always think you're more ruthless than people like me?"
A lot Manticore's nastier aristocrats (especially Pavel Young and Baron high Ridge) automatically assume that everyone is as ambitious, petty, greedy and morally bankrupt as they are, and therefore just about anything involving actual honor, loyalty or moral courage tends to trip them up.
In particular, Pavel thinks that Honor and her cronies have some demented vendetta against him, because she successfully hurt him once and enjoyed the feeling. What he can't understand is that he's the one with a vendetta, and it's so nasty that his destruction becomes a a matter of necessity.
The demons of The Riftwar Cycle are destructive, chaotic beings that don't understand anything except for ambition, hunger, and desire. The Demon KingDahun attempts to foster order, love, and loyalty among his followers in order to make them more efficient, but he ultimately fails because, as one character points out, he understood from observing humans that such things were important, but never why they were important. Child/ Miranda, a demon with a human soul, does comprehend good, but is fully aware of her unique nature and the incogruity of a demon being geniunely in love with the family of the human said soul originally belonged to, though the end of the last book indicates that she's going to return to Hell and ram love and empathy down the throats of the rest of her race whether they want it or not.
A gem from The Once and Future King: "Mordred and Agravaine thought Arthur hypocritical—as all decent men must be, if you assume that decency can’t exist."
This is a chronic failing of the villains in Fred Saberhagen's Empire of the East. The rulers of the eponymous Empire at one point attempt to bribe Ardneh into joining their side, not really understanding that there could be a being who just had no interest in the kind of power that they were offering. That being said, this trope is zig-zagged at least a little, in that at least some of them do get an inkling that Ardneh is just not like them, and has no interest in dominating anyone. They don't really understand him, but they do get that he is different from them.
Half the reason why the Big Bad in the Belisarius Series has trouble defeating Belisarius: Link can understand self-centered aristocrats just fine, and can handle groups based on statistical analysis, but an individual acting for the good of humanity? Not so much. (The other half is that Logic Cannot Comprehend Indy Ploy.)
Martha: (to Tess) You can't comprehend what it means to truly protect someone you love.
In the Star Trek episode "Mirror, Mirror", Kirk and friends manage to infiltrate the evil mirror Enterprise easily, but their mirror counterparts stand out like evil sore thumbs in our universe.
Spock: It was far easier for you, as civilized men, to behave like barbarians than it was for them to behave like civilized men.
Star Trek: The Next Generation: The Borg genuinely cannot understand why other species would rather die than join their "perfect" Hive Mind. Depending on your point of view, this may be less an example of flat-out evil and more of a Blue and Orange Morality problem: individuality is such an alien concept to the Borg that they consider it less a valid lifestyle choice and more a mess that needs cleaning up.
The Borg outlook borders on Values Dissonance, as they see assimilation as a liberating act, and can't comprehend how anyone would reject the Collective.
The end of the special "The Five Doctors", while the Second, Third and Fifth Doctors are trying to stop Borusa from becoming immortal, the First Doctor helps him achieve his goal, resulting in the villain turning into stone.
In "Doomsday", the Cybermen stage an invasion of Earth, and the Cyberleader demands a complete surrender from humanity, telling them that they will be converted into Cybermen and have their emotions, fears, and differences taken away. When humanity forms a resistance and tries to fight off the Cybermen, the cyberleader reacts with confusion; the Doctor informs it that humans aren't going to willingly surrender the very things that make them human.
In the 2005 series, the Tenth Doctor's entire plan for defeating the Master hinges on making the Master believe that he sent his companion Martha around the globe to collect the pieces of a special gun designed to completely kill a Time Lord, when her actual purpose is something far less simple and violent. And, even though the Master had fought the Doctor many times before, it works perfectly.
Inverted in Matt Smith's first finale. The Dalek presumes that since the River Song is an associate of the Doctor, she won't shoot it while it's vulnerable.
River: I'm Doctor River Song. Check your records. Dalek:Mercy? River: Say it again. Dalek:Mercy!? River: One more time. Dalek:MERCYYYY!!!
Played straight in the Daleks' previous appearance that season. They have given a robot the memories of a real human, to use as an infiltrator, and reveal that said robot is actually a bomb capable of destroying the world. They activate him, knowing the Doctor will let them flee to go save the earth. The Doctor tries to disarm the robot by reminding him of his human emotions — feelings of loss, pain and misery. Unfortunately the Daleks are perfectly familiar with this kind of emotion and it doesn't work. Amy however reminds him of love, something Daleks could never comprehend. The robot's essential humanity asserts itself and the bomb is disarmed.
The Doctor ends up in a Mexican Standoff with the Daleks in "Destiny of the Daleks": he is threatening to destroy Davros with a bomb unless they let him leave with his captive, but the Daleks respond by bringing in several human captives and exterminating them one by one until the Doctor surrenders. He threatens to set off the bomb right on the spot, but the Daleks argue that such an action would be irrational and impossible because it would kill the Doctor as well. Davros tells them that the Doctor is actually willing to do just that since "his logic is impaired by irrational sentiment".
Angel: People who don't care about anything will never understand the people who do. Hamilton: Yeah, but we won't care.
This is also the reason that the Circle of the Black Thorn make Angel sign away his role in the Shanshu Prophecy after he joins them, in an effort to prevent him betraying them for his divine reward. It never occurs to them that he would do good without the prospect of a divine reward, and that brings about their downfall.
Angelus is completely unable to understand why Angel does what he does or the "human condition," firmly believing that humans only exist to suffer and die.
In one episode of Columbo, he explains that because the killer has no conscience, she was incapable of thinking her stepdaughter would demand money as a way to expose her as the murderer rather than for the selfish reasons her stepdaughter presented.
Itassis in Mystic Force, for example, cannot comprehend how the courage of the Rangers are able to help them defeat her fellow Terrors, despite the latter being physically stronger than the former. But in a subversion, she actually betrays her people in order to learn how, being a Terror focusing more on knowledge than power.
Lord Zedd devises a plan to break up the team by capturing Kimberly and a civilian in Aisha's presence so quickly that Aisha can't do anything about it. His hope: That when the other rangers find out she did nothing will rebuke her for it and the infighting will commence. Instead they just work together to try to save them. This actually shocks Zedd.
Children of Earth, this is the attitude of the 456. Since humanity was willing to trade 12 orphans to prevent a viral pandemic in 1965, the aliens believe that Earth will give up millions of children the second time around, even after the authorities learn it would doom them to a Fate Worse than Death. When Jack Harkness claims that most of humanity would risk genocide rather than accede to the 456's demands, the aliens flat out refuse to believe him.
And just to prove how much Darker and EdgierTorchwood is, the 456 are largely right. Most humans really are pragmatic enough that they're willing to sacrifice millions of children for their own safety (at least as long as it's not their children on the line). Even Jack ends up explicitly breaking his own "an injury to one is an injury to all" ideal when he manages to defeat the 456 - by the sacrifice of a single child.
In a parallel plotline, the PM seems to think that Frobisher will be able to sacrifice his own daughters. Frobisher isn't and does indeed commit his own private genocide.
One of Cavil's major miscalculations in Battlestar Galactica was the naive assumption that just living as humans would convince the Final Five Cylons that human life was crap. He didn't even bother to give them abusive parents in their fabricated backstories. Compounded by his inability to comprehend that killing off people would cause the Final Five to mourn them, not stop loving them.
In one episode of How I Met Your Mother, Barney details the aftermath of his hooking up with Wendy, the waitress at McLaren's (the main cast's favorite bar). It ends badly when notorious-womanizer Barney can't pick up women in McLaren's without Wendy's disapproval. Wendy eventually recognizes that their hookup and quasi-attachment was a bad idea and lets Barney have his bimbos back, but Barney continues to throw out every drink she serves him because he can't comprehend that she isn't plotting some kind of revenge.
And again, in the third episode: when Tom wakes up one morning, soaked in blood, with a few hazy memories of meeting Claire the previous evening, he assumes that Hyde has murdered her: in fact, Hyde got soaked with blood while cutting Benjamin Lennox's throat- after he threatened Claire and her children.
Jekyll's a subversion of this in general, since in the end it turns out that the source of Jackman's transformations isn't malice, it's a profound sense of true love and the need to be loved in return. Hyde's sadism is destructive because it's undirected until he knows that he has a wife and children to protect.
In the Criminal Minds episode "Zoe's Reprise," the UnSub says that he is a big fan of Rossi's books, but doesn't understand what he means when Rossi says that he fundamentally doesn't understand why people choose to kill. The UnSub states that the urge to kill is normal for him; he doesn't understand why everyone else doesn't have that urge.
Season 4 episode "Who are you?", Faith has taken over Buffy's body and experiments by trying to live Buffy's life. She gets very confused and rather upset when people are nice to her. Especially Riley. It seems that "emotionally intimate and loving" is the only way Faith hasn't had sex yet.
In Season 4's "The Yoko Factor", Spike shows that he knows what The Power of Friendshipis ..., but also shows that he doesn't understand it yet. He identifies Buffy's friends as strong assets ... but is absurdly confident that he of all people can cause a permanent falling out between Buffy and the Scoobies on the eve before their big fight with Adam. Spike's sowing of discord causes a semi-dramatic quarrel that angers the Scoobies for all of a half episode. Then they rally about, and unleash epic ass-kicking. Friends fight, but friends apologize and make up too. Adam, being evil, is also waayyyy too eager to imagine that a squabble will be enough to cause a serious rift between the Slayer and her friends.
In Season 6 "Dead Things" Buffy thinks she's accidentally killed an innocent bystander. Spike wants to dispose of the evidence and sweep the matter under the rug, and can't understand why Buffy wants to turn herself into the police.
Spike: Why are you doing this to yourself? Buffy: (tearful) A girl is dead because of me. Spike: And how many people are alive because of you? How many have you saved? One dead girl doesn't tip the scale. Buffy: That's all it is to you, isn't it? Just another body! You can't understand why this is killing me, can you?
This becomes inverted when Spike says that he won't let Buffy turn herself in because he loves her. Buffy responds by savagely beating Spike, implying that she's the evil thing who can't comprehend Spike's selfless actions.
Much earlier, The Master waffles from Genre Savvy to Genre Blind with this trope. In the Pilot, The Master understands a heroic slayer well enough to know she'll risk life and limb to save Jessie, and baits his first trap for her accordingly. Twelve episodes later, the Master never pauses to consider that the Slayer herself has her own friends who will risk life and limb for her... and is blindsided accordingly. In his defense, he though he'd already finished her off.
Firefly: When Captain Mal catches up to Saffron, she claims that the reason she plays mind games and acts like a manipulative, murderous Femme Fatale is because, she believes, that's just how people are. Mal begs to differ.
Saffron: Everybody plays each other. That's all anybody ever does. We play parts. Mal: You got all kinds a learnin’ and you made me look the fool without even trying, and yet here I am with a gun to your head. That’s 'cause I've got people with me, people who trust each other, who do for each other, and ain't always looking for the advantage.
A key character trait of Dr House is his unshakable belief that people only do good things for selfish reasons. He even states that people who value others' lives more than their own are idiots. Which doesn't stop him from risking his life to save Wilson's girlfriend Amber. He fails.
On Leverage, the Big Bad of season 3 is this. He genuinely cannot understand why the protagonists are targeting him. He fails to realize that it might just be because he deserves it.
More generally many of their targets are this way in that they can't realize why anyone would go to that much trouble.
In Charmed when Cole is possessed by the Source, the rest of the demons assume he is only keeping Phoebe around because he needs someone to give birth to his son and that he only wants an heir. His secretary Julie suggests casting a spell to allow her to carry Phoebe's baby and says he would be free to rule without her love holding him back. She and the others don't seem to realise that Cole loves Phoebe and that he doesn't just want to have an heir, he's excited about being a father. Unfortunately for them, the Seer can comprehend good and uses this to her advantage.
The Seer in season 7 (played by Charisma Carpenter) is a Demon and therefore can't feel human emotion. But she knows of it through her visions - which is why she strikes a deal with the sisters to become human. This trope is arguably inverted as the sisters initially wonder why a Demon would willingly give up their powers for the things they themselves take for granted.
On Babylon 5 the Shadows brought Sheridan to Z'Ha'Dum figuring they could convert him, either willingly or forcibly. It never occurred to them until it was too late that he might crash a ship loaded with nuclear bombs into the city he was currently inside just to slow or stop them.
Regina, The Evil Queen, seems incapable of understanding good, like how Snow White's childhood mistake (that resulted in the death of Regina's lover) was not meant maliciously and how she honestly thought that Emma would leave her to die in a fire. This and her Genre Blindness are why she doesn't understand how her power in Storybrooke is weakening, nor why Gold (Rumplestiltskin), who seems to understand good quite well, is rather confident that Emma will break the curse on the town.
Regina's mother, Cora, also fails to grasp goodness. She firmly believes that love is weakness, and when she tries to steal Snow's heart, Emma jumped in front of her to save her, and this act of selfless love made Cora incapable of stealing Emma's heart because of The Power of Love
The Shield: In the Grand Finale, Vic's plan to make himself into a Karma Houdini ends up instead turning into an Ironic Hell, in part, because he honestly doesn't seem to have considered that his new bosses with a federal law enforcement agency might not want a confessed liar, thief, extortionist, drug dealer, torturer, and cop killer in anything close to a position of authority, even if they are contractually obligated to give him a paycheck.
In Noob, this seems to be a factor in the Mistaken for Badass situation between Sparadrap and Dark Avenger. Sparadrap considers that Dark Avenger and him are Friendly Enemies, while Sparadrap's Invincible Incompetent tendencies have convinced Dark Avenger that he's actually an elite player displaying Obfuscating Stupidity. Dark Avenger's standard reaction to Sparadrap's friendly lines can be summed up as "quit that little trick you use to get you opponent's guard down, it doesn't work on me.".
Eddie Kingston's 2007 and 2008 was spent beating up and destroying most of the young technicos on the CHIKARA roster, breaking Shane Storm's nose twice, bruising everyone from Tim Donst to Soldier Ant. Along comes Lince Dorado, who was beginning to become The Scrappy and is getting roundly booed by every crowd. Eddie continues the beatings on Lince, who continues to get up and keep asking for more. Kingston announces that he will never again wrestle Lince, because his tenuous grip on sanity gets confused every time Lince gets up for the people that boo him.
The sourcebookThe Book of Vile Darkness introduced the Vashar, a subrace of coldly evil humans. The Vashar are said to literally be unable to comprehend "positive" emotions, to the point that most of them wouldn't think to use a hostage as leverage, because they don't consider that the victim's friends would care about them.
Likewise, one D&D book provided DMs with the advice that a mind flayer sorcerer might be able to predict any action the heroes would take, but couldn't see that they'd be willing to perform almost certain suicide to prevent him because he doesn't care enough about anything to risk his life. Mind flayers, like the Vashar, are said to be unable experience any emotion more positive than a sort of satisfaction during feeding. This trait is even self-perpetuating; mind flayers don't learn emotion from each other, but from resonance stones, psionic deelies that emanate a specific emotion. Because the mind flayers building these can't feel love or joy, they can't build stones that project love or joy, and as such the next generation of hideous tentacle-faced monsters won't understand love and joy either.
In Changeling: The Lost, the True Fae are utterly unable to understand human motives and rationale. This isn't just a weakness, it's a defining trait — if one does start to understand a human's viewpoint, they lose most of their powers in the process, and in some cases lose their memories of their true nature outright.
This trait is potent enough that Changelings base their own government around it. The governing of their territories is routinely passed between Courts because the Fae simply cannot comprehend the idea of mutual cooperation and the willing sharing of power, which aids in concealing Changelings from the Fae.
The Deathlords have this as one of the only weaknesses in their strategic genius. As the Abyssals splatbook puts it:
Deathlords are notoriously selfish beings, almost incapable of truly understanding others. They might, for instance, do nothing more than ascribe their own thought processes to their enemies. ("Of course you returned to rescue your sister. Doing otherwise would suggest weakness in the face of your enemies!")
And then there's the Ebon Dragon. The Ebon Dragon is bastardry incarnate. Everything it does is centered around the idea of dicking someone else over. How bad is he? He had to create the Unconquered Sun just so he'd have a concept of what he was supposed to oppose. What's more, he's explicitly incapable of comprehending the motivations behind any kind of heroism save by dismissing it as abject insanity on the part of the hero. This doesn't prevent him from preying on the 'crazy heroes', because he doesn't need to understand their motivations in order to identify and manipulate their desires.
The Yozis are pretty nasty individuals and have trouble understanding that anything can operate by different rules. Their leader Malfeas has to suffer a genuine psychic fracture to understand that another being's viewpoint matters at all, and all the others are similarly limited. The Ebon Dragon knows that beings can feel positive emotions, but he doesn't understand them. He can't understand them. He will assume in any given situation that people are trying to dick everyone else over, because, well, that's what he'd do. This is simply how they work.
Most of humanity in the Warhammer 40,000 universe just want to live their lives free of war. The Orks, on the other hand, find war to be not only a bloody good time, but the only endeavor worthy of their time. To an Ork, peace is as horrible a concept as war can be to a human being.
While Magic: The Gathering avoids identifying any color wholly with good or evil, White and Black both appear to have this dynamic with each other when the designers write articles describing their perspective as though they were people. Black justifies its selfish amorality by claiming everyone else is just as selfish and amoral as it is and hates White for being a hypocrite (and admittedly also for White's dedication to Black's complete annihilation). White, on the other hand, believes that the morality it subscribes to is the basic nature of life and shared by the other colors despite their actions; in White's view, Black knows right from wrong in the exact same way White does and deliberately chooses to do wrong, making it irrevocably evil. Perhaps fittingly for their names, Black and White are the colors least capable of understanding others could possibly view the universe differently than they do. Things get interesting when White and Black are mixed.
Demons and devils in Ars Magica do not possess any of the Seven Heavenly Virtues and have to strain themselves even to imitate them briefly. This often takes them into Villain Ball territory: lacking Faith or Charity prevents them from cooperating even towards common goals, lacking Hope and Prudence undermines their long-term planning, and lacking Justice makes them relatively easy to lie to.
This constitutes the core of The Riddler's beliefs as evidenced in Batman: Arkham Asylum, with regards to Batman. To wit: he believes Batman is a Villain with Good Publicity bribing the Gotham Police Department and stealing money from the crooks he captures, because "no one's that selfless."
Likewise, in Batman: Arkham Origins, the Joker is completely baffled over why Batman chose to save him from falling to his death. The GCPD are also confused, deciding that the only reason Batman would "jump off a building to save the Joker's sorry ass" is that they must be partners.
Demi-god Vivec's Batman Gambit to defeat Dagoth Ur. Both Vivec and Dagoth Ur draw their strength from the Heart of Lorkhan. The player acquires a set of items able to manipulate its energies, and Dagoth Ur assumes you intend to use them to make yourself immortal as well. He spends his energy taunting the player about his own power, not realizing until the very end that the player's goal is actually to unbind the Heart, denying its power to anyone.
Shepard wins for two reasons: first, the Reapers underestimate just how Badass s/he and his/her team are, but second and more importantly because they can't comprehend the fact that Shepard is willing to throw him/herself into almost certain death for the sake of others.
If playing Paragon!Shep, the Illusive Man makes a similar mistake by not having any backup plan to seize the Collector base when Shepard decides to blow it other than relying on Miranda (and possibly the rest of the Cerberus personnel on the Normandy) to get it for him. He apparently completely underestimates the loyalty they have in Shepard for making sure No One Gets Left Behind.
Of course, this is largely due to it being a stated Suicide Mission, and TIM didn't realize it could be done until after EDI sent him the schematics.
The Reapers also fail to predict that the Protheans might choose to sabotage their next attack rather than fighting to the last man to survive the current one, and their efforts to keep an alliance from happening in Mass Effect 3 by pressing on the borders of all the major species run into trouble when the various races ultimately prove willing to support the overall plan rather than protect their own borders at the expense of everyone else. Then comes the Miracle at Palaven, when they don't predict commandoes willingly accepting their own deaths rather than risking indoctrination while placing nuclear weapons inside their carapaces. Really, the most common cause of Reaper defeat and inconvenience is that they assume everyone else is as devoted to self-preservation as they are and thus get caught with their kilometer-long pants down by a Heroic Sacrifice.
In Final Fantasy V, when Galuf's Berserk Button gets pressed and he charges Exdeath in one-on-one battle, the villain comments that "not even all the hatred in the world can destroy me!" Sure enough, Exdeath gets his ass beaten because it wasn't hate, but something else entirely that made Galuf fight on while at zero hit points.
Completely inverted with Sargeras, the creator and leader of the Burning Legion. Originally belonging to a race of god-like beings called the Titans, he and his kind traveled throughout the cosmos to bring order to worlds; they were so powerful they defeated the Old Gods, the Eldritch Abominations of Azeroth, and created the dragons to become the world's stewards. While defeating and imprisoning the demons of the Twisting Nether, their evil caused Sargeras to question the Titans' quest for order. He was driven into depression after witnessing the chaos wrought by the demons, especially after defeating the vampiric Nathrezim, whose manipulative bastardy on various worlds affected him deeply. Eventually, he went completely off the rails with the belief that the Titans' quest for order was essentially wrong, given that he saw the Universe as intrinsically chaotic and evil. The last the Titans saw him, Sargeras had freed the demons he had personally previously imprisoned, made them a part of his army, and sent his Burning Legion to bring war upon the Universe, putting into action the corruption of the Draenei and Orcs, the birth of the Lich King, and the multiple near-destruction of Azeroth itself. An example of Good Cannot Comprehend Evil taken to epic proportions.
Then again, the Legion itself seems time and time again to be unable to comprehend mortal beings. They never seem to consider the possibility of mortals putting aside their hatreds for each other to fight the Legion, nor did they predict that the Lich King would turn against them instead of submitting to his new position as a tool of the Legion (essentially, a lesser being defying them).
Played with by the Nathrezim, who are Dangerously Genre Savvy enough to wage warfare at a distance, stoking up conflict between factions to distract them from the real threat, and manipulate useful pawns to enact their will with plausible deniability. This does not stop them from making slip-ups of this variety on occasion. One happens when their leader, Mal'Ganis, assumes Evil Prince-in-training Arthas won't exact revenge on him for leading the destruction of Arthas' homeland of Lordaeron and forcing him into a Sadistic Choice at the town of Stratholme, since Arthas' soul was just consumed by his new weapon, Frostmourne. But having no soul does not prevent Arthas from enacting his revenge upon his opponent. At all.
A particularly famous example occurs when Grom Hellscream stands against Mannoroth, the demon whose blood he drank on two separate occasions, setting the stage for his clan - and separately, his race - to become thralls of Mannoroth's demon masters. After swatting aside Grom's brother-in-arms Thrall, Mannoroth boasts about the part he played in Grom's corruption and mockingly declares they are the same. (Mannoroth was a tyrannical ruler of his race who willing joined the Legion and served as a frontline commander during the War Of The Ancients.) In a dramatic moment equal parts Big "NO!" and Shut Up, Hannibal!, Grom buries his axe deep into Mannoroth's chest at the cost of his own life, a clear statement that they are not.
Should the player character decide to take the good ending in BioShockFontaine rants about how he created Jack, made up his memories and stuffed them into his brain, showed him the world, brought him back to Rapture - "If that's not family, I don't what is!" - shortly before the Little Sisters appear and demonstrate what family really means. With needles.
While subtitled, Spyro the Dragon's Malefor is clearly caught off guard when Cynder is freed from his mind control by the Power of Love. In the entire battle, this is about the only thing that actually seems to truly surprise him.
Similar to the Joker's "social experiment" in The Dark Knight, Hot Coldman had programmed Peace Walker's Mammal Pod to transmit the same false ballistic trajectory data that was going to trick Peace Walker into going into nuclear retaliatory launch mode to NORAD, at a time when the President and most of the Executive branch was out at Vladivostok at the time, to essentially force the military to decide whether to retaliate or not based on the data. His intention for this Sadistic Choice was to prove that humans were too weak-willed to actually retaliate, even when the enemy is going to launch, and thus make a machine to make all those decisions. However, Coldman did not anticipate that they would actually go through with doing a retaliatory strike, though going by Coldman's last words, its very likely that he probably didn't care either way, and he certainly did not count on Peace Walker actually choosing to sacrifice itself by drowning/shorting out its electronics than keep it going.
Disgaea 2: Cursed Memories: Rozalin cannot understand why Adel would want to escort her home instead of using her as a pawn in his own plans. She is willing to fight to protect Hanako and Taro, but believes she's only doing that because they are her "vassals", and caring for your vassals is what nobles are required to do.
Mao in Disgaea 3: Absence of Justice has this problem. Despite his obsessive research on super hero tropes, cliches, and plot devices, he just doesn't get stuff like love and courage. He knows they exist, but can't make heads or tails of them.
This was ultimately Ghetsis' downfall. His own dialog shows he personally believed everyone saw Pokemon as tools, just as he did. Because of this, he allows his son N to encounter Pokemon that had a truly caring relationship with their trainers, causing N to question Team Plasma's cause and befriend the player character, whom Ghetsis continuously underestimates because he doesn't believe they can behave selflessly and/or care about their Pokemon. As a result, the player acquires the other legendary dragon, defeats N, and for a nice bonus personally curbstomps Ghetsis with The Power of Friendship. Cue screaming breakdown.
Bites Ghetsis again in the sequels, where he insists to himself aloud, on-screen, that Pokemon (and "that inhuman freak" N) aren't sentient and so can't hate him, only serve him. Right in front of two trainers, at least half a dozen Pokemon, two legendary dragons, and one "inhuman freak", none of whom agree with him. He also dismisses Colress's research verifying The Power of Friendship, despite having personally hired Colress to study how best to make Pokemon powerful and lead Team Plasma in his stead.
Implied in Dungeon Keeper, especially the first game. Before each mission, The Evil Mentor gives you a brief introduction to the land you're about to conquer. He seems both revolted and amazed by the happy, peaceful, non-violent lives the peasants are able to lead. One town, for example, is described as 'a truly bizarre realm' because the inhabitants prefer talking, laughing and singing over arguing, drawing daggers and murdering each other in a gurgling rush of blood.
Sagacious Zu manages to trick Death's Hand into burying himself in Jade Empire because Death's Hand wasn't prepared for the possibility that his foe would sacrifice himself to complete his goal.
This is the key to success in I Have No Mouth and I Must Scream. Each of the initial five scenarios are prepared with AM assuming his captives would fall victim to their baser desires, but to complete them each character has to overcome their flaws and make sacrifices, which utterly baffles the mad AI, who can not see humans as anything but utter bastards. In the endgame, you have to defeat three computers representing AM's Ego, Superego and Id. Using the Forgiveness totem on the Ego causes him to shut down, since he can't comprehend how anyone would forgive him for all he's done.
Super Paper Mario: Dimentio simply thought that, after the heroes used up the Pure Hearts to defeat Bleck, they would be gone for good, thus meaning the only threat to him after backstabbing a weakened Count Bleck and gaining the Chaos Heart would be forever gone. As such, he ends up legitimately surprised when the Pure Hearts return (thanks to the love between Bleck, Tippi/Timpani, and his followers) and remove his invulnerability.
Fear Effect: Yim Lau Wong (The King of Hell) turns out to have no concept of human decency. If you make the choice to not have Hana and Glas shoot each other, The King of Hell will fly into a rage and say "Mei Yun, you have come too far to disappoint me!"
Played for laughs in Knights of the Old Republic 2 with HK-47. The player has the option of installing something that turns out to be a pacifistic program, which they will uninstall after the ensuing hilarity of a the Ax-Crazy droid saying he couldn't harm another living thing. After expressing disgust at the thought that he nearly surrendered to peace and pacifism, HK-47 comments "It was close, but for a moment I thought I understood why some meatbags would prefer friendship over a high-powered blaster carbine." Apparently he can't grasp why anybody would not want to kill someone.
The Big Bad of Persona 4, Izanami, expresses her disbelief that "the will of so few could surpass the will of so many" in regards to the protagonist's Social Links. She also can't understand why humans wouldn't want to live in ignorance.
Evil in general doesn't seem to have any real problems with understanding good in Star Control. The Neo-Dnyarri gets bitten in the ass by self-serving pointlessly cruel evil not being able to get honourable evil, though: it sends you against the most powerful race in the region to get killed. That would be fine... except that race happens to have been enslaved by the Dnyarri and with the sort of sense of honor that would let you just leave the area unmolested (once) for warning them about the Dnyarri returning.
Despite his alchemical and tactical genius, Hazama/Terumi Yuuki from BlazBlue either considers the spirit of goodness (and what motivates people into doing good) a means to use people to serve his whims (like Litchi and Tsubaki) or considers it shitty and boring, if he understands it at all. In the Slight Hope story from Extend, however, this bites him square in the ass. He was merrily carrying out his plans in the Wheel of Fortune timeline when Makoto Nanaya fell in from the Continuum Shift timeline, and when she got beat up after parrying a hit on Jin, he dismissed her as merely a "damned squirrel" best left to Relius. Between that incident, honesty to Tager and Kokonoe regarding her intentions, trusting Bang with rescuing Jin, and counseling Tsubaki (and asking her about the unknown-to-Makoto nonexistent Noel Vermillion), she altered the timeline in a way that caused Hazama's plans to implode - even he was forced to admit asking Tsubaki about Noel caused it to self-destruct. Given his assassination attempt on her in Continuum Shift proper, which takes place days later, he has never forgiven her for this insult. And yet, despite all that, it has done nothing to his opinion on goodness, much less make him stop acting like scum. All he really learned is to let his buddy Relius take care of her... so what happens if he can't deter her?
Caesar's big mistake is that he arrogantly assumes that any resourceful and competent person must obviously agree with his worldview and invites the Courier to work for him. It doesn't matter if the Courier is a goody-two-shoes dedicated to protecting the downtrodden and needy, and so far have focused their efforts on supporting the NCR and messing up the Legion's plans. He will assume you will agree with his brutal regime purely because you are a capable badass, and task you with vital missions without making even a token effort to change or even acknowledge your past allegiances. The biggest moment of this comes after you pretend to destroy House's bunker, and Caesar offers to repay you by killing Benny. If you try to release him Caesar will chastise you for not enjoying violence and blackmail you into killing Benny yourself by threatening to crucify him. And after all that effort to manipulate you into doing something you clearly didn't want to? He smugly boasts about how sure he is you loved it.
In the epilogue of the Dead Money DLC, if Dean Domino, whose manipulations before the war were pretty much why the Sierra Madre is a hellhole, is still alive he'll learn of how his former accomplice Vera Keyes was addicted to Med-X and Super Stimpacks (which he used to blackmail her) due to a terminal illness and the story of how Sinclair tried to sacrifice himself to save her. It's stated that he felt strangely sad for a moment but has no idea why. It's at least enough to make Dean finally let go of the Sierra Madre...and set his sights on New Vegas. The backstory of the DLC also shows that Dean saw Sinclair's happiness as a form of self-righteousness and that he felt as if Sinclair was simply rubbing his success in his face.
In the Old World Blues DLC it's possible to get Evilutionary Biologist Dr. Borous to feel tremendous guilt about how he treated Gabe, his beloved dog who was loyal to the very end, as a test subject that he subjected to countless experiments (including turning him into a Cyberdog and pumping him full of combat drugs). When it finally hits him, he has no idea why he suddenly feels so horrible, deciding that he doesn't like this feeling and quickly suppresses it, though it's hinted that it still lingers.
In Radiant Historia, the Big BadHeiss, Stocke's uncle, cannot comprehend in the true ending why Stocke is willing to be the Sacrifice unlike himself. Stocke explains that, ironically enough, it's because of the Big Bad. Heiss raised him with earnest love as his nephew and introduced him to people he would treasure as his friends. Unlike Heiss, Stocke had people he cared about enough to give up his own life to protect. In a twist, Stocke's words reach Heiss and Heiss offers himself as the Sacrifice to save Stocke.
Handsome Jack of Borderlands 2 has an understanding of "good" that is at the very least incredibly skewed and deeply delusional. He honestly believes himself to be a hero attempting to bring civilization to Pandora while at the same time gleefully relishing torture and laughing about a time he gouged out a man's eyeballs in front of his children. He seems to believe that being a hero is simply being rich and powerful enough to kill anyone you don't like.
In Dishonored, if Corvo spares Daud, the assassin who murdered his beloved Empress,the Outsider is utterly shocked. This is the only thing that will surprise the Outsider. It doesn't do anything to change his low opinion of humanity as a whole; he merely considers Corvo to be an exception to the rule.
In Kingdom Hearts 3D [Dream Drop Distance] Xigbar proves just how much he doesn't get it by trying to induce a Heroic BSOD in Sora by telling him that since his friends are his power, Sora has no real power of his own. This only manages to affirm Sora's belief in The Power of Friendship, since that means he's part of something much bigger. Xigbar is utterly baffled by Sora's reaction.
Even earlier than that, in the first game, "Ansem"/Xehanort believes that darkness is the heart's true essence and thus, Kingdom Hearts, as the most powerful heart, must have the power of supreme darkness. Thus, when he tries to harness the power of Kingdom Hearts, he instead gets blasted by its light.
Infamous 2: Nix. She always advocates the Evil Karma decisions for Cole, and whenever someone else suggests a goal that involves helping people and getting them to fight by Cole's side willingly, Nix not only scoffs at it, but acts like they're crazy for even thinking of it. From what she tells us of her childhood, she probably hasn't met too many nice people in her life.
The Legend of Zelda: Skyward Sword: As the only humans he faced prior to Link were cowardly and either hid or turned to Hylia for protection when faced with him, Ghirahim is utterly perplexed that Link keeps ignoring his threats and challenging him. Demise is also taken aback by this, but he's more amused by it than anything. It's more along the lines of Evil Cannot Comprehend Courage, but the basic idea is the same.
Happens during the Very Definitely Final Dungeon in Tales of Symphonia, where the Big Bad kidnaps the party except for Lloyd and attempts to Mind Rape them by torturing them with their personal demons (all of which the Big Bad can also relate to, as he's suffering from the same kind as them.) Lloyd manages to find them and help them confront and overcome each of them (involving forgiveness, courage and acceptance,) leaving the Big Bad dumbfounded each time.
Devil May Cry 4: Sanctus repeatedly scoffs at the concept is love, even explicitly deriving Credo's love for his sister Kyrie as foolish. Unfortunately for him, it's this view that, according to Dante and Nero, renders him unable to truly harness the power of Sparda's sword.
Completely subverted in Fate/stay night in Heaven's Feel. Despite trying to destroy the world in large part For the Evulz, the reason Kotomine decided the reason he would do that is he understood good perfectly well. He's just unable to actually do it and feel satisfied no matter how hard he tries. Apart from his background material, he gambles away his entire magic crest to save Sakura knowing that Shirou's righteous spirit will make him protect her from anything. In fact, his Xanatos Speed Chess was entirely reliant on exploiting the 'good' nature of Shirou.
When everyone confronts the Mastermind at the end of Danganronpa. Junko, being pretty much despair personified, manages to get everyone to cross the Despair Event Horizon by revealing that the world outside the school has been destroyed, and all their efforts to escape have been for nothing, as there's no guarantee they'll even survive if they step outside. Naegi, having become Super High School Level Hope at this point, manages to give everyone their Heroic Second Wind, to which Junko freaks out and screams "What the hell are you!?"
Earlier, Byakuya is utterly shocked when he he misses a crucial detail involving Sakura's death, while Naegi manages to discern it with ease, and completely flips when he learns the reason: he never imagined that Sakura would commit suicide in order to protect her friend.
A rather bizzare subversion occurs in Goblins. When Kore, a Knight Templar Extraordinare chases a group of goblins and takes one of them prisoner, he proceeds to torture him, (correctly) expecting the others to hear the screams and try and save their comrade. However, judging from his uncompromising approach to "evil" races, you'd think he'd consider such "irredeemably corrupt and wicked beasts" as goblins to be incapable of selflessness and comradeship.
Redcloak assumed that the humans would think highly of the goblins who spared them and despise the paladin who did not save them. In fact, the humans were heartened by the paladin's resistance to Redcloak.
That strip shows the real problem the humans and goblins have with each other - neither sees the good in the other.
Earlier, in #69 the following exchange occurs after Elan saves his brother from falling:
Nale: I'll never tell you anything about Xykon. Elan: Yeah, I know. But I didn't save you so we could interrogate you. I saved you 'cause I'm the Good twin, not the Neutral twin. Nale: ...I don't get it. Elan: Yup.
A protagonist example in #523, in which Belkar is unable to understand the benefit in freeing slaves.
In Start of Darkness, Xykon defeats Dorukan and seals his soul within a gem along with the soul of former teammate Lirian. His only understanding of love being mostly just sex and rape, he just assumes that this is And I Must Scream. However, he actually unites the souls of two lovers for eternity.
Similarly here. No, it's not that weird that Elan doesn't like watching people suffer just because they got the better of him once.
In Strip 880, it's how Haley knows that Belkar's telling the truth about Durkon having been killed and turned into a vampire by Malak. She knows that Belkar couldn't make up the part about Durkon's last wish being for Malak to spare the rest of the Order, since Belkar couldn't conceive of anyone being that selfless.
A group of politicians dig up an old, unfulfilled contract involving ancient relics to seize Quentyn's old hometown. Quentyn pulls the thread on the whole thing by going out to try and fulfill the contract, even if it takes him the rest of his life. Because of laws concerning such contracts, even if he dies trying, the contract is canceled.
In fact, a few comics later, other characters outright state this trope. The politicians have no answer to the heroic sacrifice, because when they started their bid to take over the town they completely overlooked the possibility that this could happen.
"[The Hero] made a move that they completely failed to prepare for. Unsurprising, I've found that schemers and plotters are rarely able to cope with simple things like honor and courage."
Girl Genius: Baron Wulfenbach is definitely an antagonist, though perhaps not an outright villain. However, he can't understand that some things don't have a sinster ulterior motive behind them. For example, when an opponent allows his severely battered army to withdraw from the battlefield, he immediately sends out scouts to search for the flanking force preparing to destroy them they must have missed. That his opponent is genuinely trying to avoid further bloodshed never even crosses his mind.
To be fair, such a thing is pretty unprecedented in the setting.
Grim Tales from Down Below: Him is upset when his daughter betrayed him but not at the betrayal itself, but the reason for Mimi's betrayal is for the lover of her friend. Him even said that if she betrayed him for petty reasons, he would've been proud.
Unlike most examples of this trope, Ma-Ti has known the Critic first hand as a colossal, selfish, JerkassMan Child. His shock is more understandable under the circumstances, making it more of a case of Evil Cannot Comprehend Character Development.
In one Global Guardians story, it was the titular hero team who invoked this trope. They were literally handed the exact location of Osama bin-Ladin and the rest of al-Queda's leadership by Lord Doom, one of their greatest enemies shortly after the 9/11 attacks and the fall of the World Trade Center (an event that took the life of one of their teammates). It took the Global Guardians nearly a week to take advantage of this intelligence because they could not think of a reason for Doom to help them that didn't involve an ulterior motive, a trap, or a distraction from some bigger scheme. Turns out, Doom helped them out of a sense of horror, disgust, and anger for al-Queda's targeting "innocent bystanders".
This moment of her inability to comprehend that love can trump self-preservation and loyalty born of intimidation has limits, flying in the face of her philosophy that "fear is the only reliable way" to control people, is actually the first step down the road towards her epic Villainous Breakdown. However, because she's Dangerously Genre Savvy, she's at least able to learn from this mistake and apply it to her strategy in the Grand Finale (while she was in the middle of said breakdown no less).
This becomes somewhat of a running theme for Mai. In the comic Rebound, her father is confident she'll want to join his movement to overthrow Zuko after she breaks up with him. He never expected his freedom fighters would be Mai's terrorists and miscalculates her response as badly as Azula did.
Azulon does not expect Mama Bear Ursa to try to take him out in order to save her son's life... much less succeed.
Firelord Ozai did not expect Zuko's refusal to fight in the Agni Kai. Zuko was willing to fight a general, but not the father he loved.
Firelord Ozai cannot fathom why Aang spares him at the end of their fight.
In episode "The Beach," Mai, Ty Lee, Zuko, and Azula all take turns confessing their problems, and helping each other talk through their issues. When it's over, Zuko and Mai have reconciled over an argument they had and Ty Lee feels cleansed. Azula compliments them on their great "acting", treating the entire thing like it was a show.
In season 1, XANA's flawed understanding of human behavior, including things like courage and friendship, is his major flaw. In one episode, he traps the team in a virtual Matrix-style copy of the school, forcing Jérémie to virtualize himself to warn them. This leads to a Spot the Imposter scene where XANA (disguised as Jérémie) tries to convince the others how Jérémie's story can't be true:
XANA: Everyone knows that the real Jérémie wouldn't step foot in the scanner. He'd be much too frightened! Odd: (after a pause) And I'm sure he would go into the scanner... if his friends were in danger. Ulrich: No doubt about it. Yumi: Absolutely none. XANA: But it's not logical! Don't you see? He's much too scared to even try... I—I'm much too scared! If not, then why haven't I already done it? Jérémie: I told you why. Because he's not infallible. XANA's knowledge of people is only approximative. Odd: And when it comes to friendship, it's not approximative; it's double zero. Good to see you again, Einstein. (Jeremie smiles.) XANA:No, it's not logical! NOOO!NOT! LOGICAL! NOT! LOGICAL!
In the Justice League Unlimited episode "For the Man Who Has Everything" (based on a story from the comics), Mongul imagines that Superman's greatest desire being shown to him by the Black Mercy is of him ruling the galaxy. Instead, he's living peacefully on a farm on Krypton, married to a woman who resembles both Lana and Lois, and has a son.
When the Mad Hatter imprisons Batman in a fake world where his parents were never killed and he's engaged to Selina Kyle, who isn't a criminal. It's practically a paradise. When The Mad Hatter asks him why he chose to escape, he responds with "Because it's not REAL."
Both subverts and plays this straight with the relationship between David Xanatos and Fox. Though there are signs of their affection as early as Season 2's "Leader of the Pack", Xanatos doesn't initially believe their attraction and compatibility could actually be called love because "two people such as ourselves are [not fully] capable of that emotion."... until "Eye of the Beholder" has him going through plan after plan to get the woman he loves back after she has a bad experience with the Eye of Odin.
Xanatos: So now you know my weakness. Goliath: Only you would regard love as a weakness.
Duncan, Demona, and Tony Dracon also play the trope straight; Duncan's and Demona's treacherous natures led them to suspect that the loyal, honest Macbeth was equally treacherous in "City of Stone" Part 3 (in Duncan's case) and Part 4 (in Demona's case), while Dracon suspected the same of Elisa in "Protection."
Oberon doesn't seem to realize how everyone would fight him to keep him from taking away Xanatos and Fox's child. Given the implication that Titania (who put the idea in Oberon's head to kidnap the baby) did the entire thing to get Fox to tap her fey powers in anger, it's suggested that Titania did.
Played straight in the "Toilet Paper" episode. Cartman is simply incapable of comprehending why the other boys feel guilt about Butters getting busted for what they did. He later confesses, but only in hopes of either getting lighter punishment, avoiding punishment, and looking good to the adults. Depressingly, because the adults are ignorant of Cartman's mental state the ruse works.
On the other hand, it shows to the viewer that yes, coming clean sooner is good for you; it's just that this time the wrong person came clean for the wrong reasons.
This extends to the point that Cartman actually believes he did learn a valuable life lesson and tries very awkwardly to deliver An Aesop, much to the exasperation of Kyle.
Cartman: I've learnt that while you might not get in trouble first, you can later. Kyle: *Face Palm* Oh god... Cartman: At first I didn't feel bad but now I feel terrible. Kyle: You just feel bad for yourself because you got put in detention! Cartman: Right, so I guess what I learnt today is... Kyle: Oh stop it, Cartman. You didn't learn anything! Not a Goddamn thing!
The Coon and Friends trilogy demonstrates this with a short dialogue between "The Coon" (Cartman) and Mysterion (Kenny). (And the debate with the Ayn Rand Foundation begins...).
The Coon: It's not my fault you guys turned evil, Kenny. Mysterion: You are the bad guy, Cartman. You! The Coon: I'm making the world a better place! Mysterion:FOR YOU! You're making it a better place for you! The Coon: (Beat) Riiight. That's what superheroes do.
Possibly subverted in "How to Eat With Your Butt". Cartman loses his ability to laugh after seeing the Thompsons, people with a condition that makes their faces resemble buttocks. The other boys claim this is because he feels genuinely sorry for them because they lost their son, but Cartman insists the sight was so funny he merely "blew a funny fuse". When their son (Ben Affleck) is reunited with them, the sight of them "kissing" him causes him to laugh again. He says it is so hilarious that it fixed him, but again the others tell him it's because he is happy they are back together. The subversion depends on whether or not he really felt sympathy for them (and was merely unable to comprehend why), or he didn't (and couldn't understand why he should).
Also played straight in an episode of She-Ra: Princess of Power. Forced to work together, She-Ra and Hordak get directions from a local in exchange for some fruit that's trivial for them to get, but impossible for the local to reach. Hordak starts to go the other way from the directions, saying the local had what he wanted, and thus no reason to genuinely help them.
She-Ra: Your problem, Hordak, is that you lie all the time, so you assume everyone else does the same, even though you depend on most people keeping their word.
This is frequently where Him's plans go wrong on The Powerpuff Girls. Every time he creates a situation to exploit something like their anger or fear, he's shocked at how sisterly love helps them overcome it. When Blossom and Buttercup save Bubbles in "Octi-Evil" after he thought he'd broken them up: "But you're supposed to be fighting each other!"
In an episode of The Smurfs, Smurfette meets a very greedy troll who has a hard time understanding why anyone would give something of theirs away; this happens on her birthday, when the other smurfs are giving her gifts (he proceeds to steal them all, and Smurfette herself). After being rescued, Smurfette proves to be a lot more generous (not to mention forgiving) than he is, and he starts to learn his lesson after she shares with him.
As noted by Rob Hoegee in a feature on the Third Season DVD, this trope is Slade's achilles heel. His inability to understand Robin's willingness to sacrifice himself for his friends at the end of the first season or Terra's residual loyalty to the team in the second proved to be his undoing. It's worth noting that when his opponent is Trigon, the literal embodiment of evil, Slade's plan really goes off without a hitch, largely because Trigon acts in exactly the ways he predicts.
Trigon has the exact same weakness. Trigon couldn't understand why, against all odds, with the world literally having ended, the Titans continue to fight him and why Raven, despite him being her creator stands up against him. This is ultimately his downfall as well.
In "Last Exit to Springfield" Mr. Burns cuts the power to the town during a strike, and is shocked that the union doesn't break.
After learning about recycling from Lisa in "The Old Man and the Lisa", Mr. Burns takes it to its extreme by recycling living sea creatures into a multipurpose slurry. He doesn't understand why Lisa is horrified by this, since, as he sees it, he is giving people what they need without wasting a single sea creature.
Happens with Jessica Lovejoy in "Bart's Girlfriend" after she was caught framing Bart Simpson and stealing the church collection plate money. When she saw Bart approach her while doing her punishment of washing the church steps, she assumed Bart was going to laugh at her. He instead confessed how their small relationship taught him not to be naive around girls. Jessica, however, confessed that she learned she could make boys do whatever she wanted and proves it by asking Bart to finish the job while she runs off with another boy. Bart pretends to fall for it, so he could give her a final Take That.
Part of Vicky's Flanderization, as shown in "Frenemy Mine", is she cannot understand love, to the point where she cannot comprehend her feelings after Timmy saves her.
An even better example are the Yugopotamians, a race of aliens who find any form of love or compassion absolutely terrifying and to whom hugs, chocolate, and fuzzy toys are a health hazard.
In an episode of He-Man and the Masters of the Universe (1983) where He-Man and Skeletor are forced into an Enemy Mine situation in order to save Eternia, Skeletor tries in vain to comprehend doing something good for a change. He asks He-Man "Don't you ever feel like doing something evil?" He-Man answers "Don't you ever feel like doing something good?"
General Zhal from Batman: The Brave and the Bold is left completely stunned after he kills the Doom Patrol and the entire world chants "We are the Doom Patrol", showing that instead of making everyone see them as frauds, they see them as bigger heroes than before. Zhal is unable to even react to being arrested out of shock because he can't understand how a Heroic Sacrifice increases people's faith in the sacrificer.
The biggest weakness of Discord is his inability to truly understand how strong the bond between the mane cast truly is. He's taken completely off-guard when he discovers that they've reforged their friendship after he seemingly broke it apart leading to his defeat. He also gets very frustrated when Fluttershy proves too kind and accepting of her own faults to fall for his attempt to convince her her friends think she's weak and helpless and thus she should be mad at them. This makes sense when one considers he's the polar opposite of the Elements of Harmony, which run on the Power of Friendship. It may also be another of the apparent Shout Outs to Him, who shared this weakness as well. Ironically, in his second appearance he not only manages to comprehend it in the end, the act of doing so is what redeems him, as his new found friendship with Fluttershy makes him unable to bring himself to do anything to jeopardize it.
Queen Chrysalis, the Big Bad of the second Season Finale, also has this problem. She's a sadistic, shapeshifting, succubus-likeHive Queen who stole Princess Cadence's identity to feed off the love her husband to be had for her. In the end, she doesn't once think that this same power could be turned against her. To her, it was just food and she didn't truly understand its true power.
In My Little Pony Equestria Girls, when Sunset threatens to destroy the portal back to Equestria if Twilight doesn't hand over the Element of Magic, she is shocked when Twilight refuses, knowing what Sunset could do with it. Sunset never expected Twilight to jeopardize her way home to protect a world that wasn't hers.
In Twilight's Kingdom Part 1, during his Breaking Speech to Discord, Tirek dismisses his brother's befriending ponies so many years ago as a sign of a weak mind. More generally, he considers friendship just another form of imprisonment.
In Twilight's Kingdom Part 2, Tirek cannot understand friendship, and is confused when Twilight demands Discord's release after he betrayed them. It is this mistake that leads to his defeat and re-imprisonment for eternity.
In How To Train Your Dragon 2, as Drago Bludvist sees it, dragons can only be controlled through intimidation and fear. Working with dragons, nurturing them instead of enslaving them, is unthinkable to him. Exemplified when Toothless overrides the Dark Alpha's control to protect Hiccup.
In the Christian-based cartoon God Rocks a robot kept on trying to ruin the God Rocks concert to raise money for a good cause, and he didn't understand that even after he stole their instruments they still desired to play.
In one episode of the Battletech animated series, Mechwarrior Ciro forces a jumpship captain at gunpoint to record a message to Adam Steiner, saying that he knows where Adam's missing-in-action brother is, in an effort to lure Adam into a trap. Nicolai Malthus asks why Adam would respond to such a message, and Ciro replies that Adam would do anything to help his brother. It's a reaction Malthus finds impossible to understand. This is fully understandable, however, in that Clan Mechwarriors don't have families, they have sibkin - other Clan Mechwarriors who were created by scientists and incubated in artificial wombs. Though the bond between sibkin is stronger than the average bond between two different members of the same clan, they still view one another as only allies at best, and frequently as rivals competing for status and a limited number of choice assignments. To earn their status as Mechwarriors, they have to begin by emerging victorious in duels - and the losers get crap assignments or even demoted to a lesser caste! While many of them would understand the idea of complete and blind loyalty to another, few of them would feel it; and Nicolai is not exactly the most well-adjusted Clanner to begin with.
Roger of American Dad!, due to his species practically being Made of Evil, is completely unfamiliar with the idea of feeling for anyone over himself. So much that actually feeling guilt over one of his acts was such a trauma to his state of mind, it created a split personality out of it just to cope.
Say what you will about Ultimate Spider-Man, however one such episode worth mentioning is "Strange Days", in which the villain Nightmare forces everyone on Earth to be trapped in a permanent dream facing their worst fears. In the end, Spider-Man is the last to be forced to face his deepest fear, by making him face disappointment from his Uncle Ben over his death. Instead, the dream-version of his uncle greets him with a smile. Spidey then talks back at the confused Nightmare, saying he lives with what happened everyday and instead of letting it get to him, he lets it encourage him to be Spider-Man everyday. This in turn is what starts Nightmare's plan to go apart because it never occurred to him someone has the will to overcome or accept their fears.
Also happens to the Light in the same episode. They never thought that Artemis, Miss Martian, and Superboy would willingly reveal their Dark Secrets to the rest of the team, and that the team would fully accept them. Because of this, the Light gets Out-Gambitted.
In an episode of Codename: Kids Next Door, Nigel wakes up in a world where he's an adult and president and his teammates are all part of his cabinet. The Alternate Hoagie eventually realizes what's going on and agrees to send him home if he'll sign the bill that would destroy their world's Kids Next Door. Nigel refuses, even when threatened. Hoagie doesn't get why, since he'll never see the kids he's sacrificing again and it won't effect his world.
On Yin Yang Yo, the Night Master accurately assesses that the titular trio have a lot of undesirable, un-heroic qualities. However, he scoffs at the idea that they could rise above them and become better people. He also clearly wasn't expecting Coop to accept Yin's apology and turn on him.
And then there's Mirage. She's firmly convinced that she can ruin Aladdin and Jasmine's relationship by transforming Jasmine into a hideous snake woman and then destroying the only antidote. Aladdin's response is to transform himself into a hideous snake man in order to be with Jasmine, which was the last thing Mirage ever expected.
Ragnar of Green Lantern: The Animated Series worshiped the Green Lantern of his planet. Believing himself to be worthy of a Green Lantern, he poisoned him and attempted to claim his ring. Instead, his sister, Queen Iolande, became the Green Lantern. His jealousy and feelings of betrayal lead him to become a Red Lantern. It never occurred to him that his murdering a Green Lantern and his desire to abuse the power of one were the very reasons he was rejected.