In Dragon Bones, none of the villains is able to understand that some member of the Hurog family would not kill or otherwise sacrifice their own family members in order to become Hurogmeten instead of the Hurogmeten. Thus, Ward is easily able to pretend that, of course, he will kill his uncle to get the castle back.
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. It's a running theme of the book.
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.
Grima Wormtongue and Saruman are each extremely bewildered by mercy shown them by their enemies, and Saruman sees Frodo with great respect (and all the more hate for it) after Frodo lets him go.
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 President's Vampire, Wayman can't understand why Griff, who's dying of cancer, won't use the Elixir of Life (made of Human Resources and created by a Nazi) to save himself. When Griffin tells him that there are some values you'd never sell for anything, he's even more baffled.
In David Edding's The 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.
In The Great Pacific War, the Japanese government makes this error. They've been interfering in China and supplying arms to rebellious warlords, and they see a US mining company winning a contract there as a front for the US government to interfere in China and supply arms to the government, even though no such thing is happening.
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 switches sides because Voldemort killed Lily, and Narcissa Malfoy withholds key information from Voldemort to protect her son.
It's not just Voldemort and his mooks who are like this. In the second book, GilderoyLockhart is so narcissistic that the thought never crosses his mind that Harry doesn't seek fame like he does.
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".
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 worst 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."
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 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.
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.
Reacher Gilt from Going Postal doesn't seem to understand the concept of trust or belief at all and just marvels at how easy everyone else is to fool. He also doesn't understand Vetinari's 'angels' speech, which leads him to choose the door.
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.
Only in Death: Soric's keepers from the Black Ships think that he might kill Hark. (Hark, although he would not blame him if he did, knows that he is safe.)
Salvation's Reach: Due to his one-sided grudge against Gaunt, Meryn just doesn't get the other man and thinks Gaunt's all about ceremony and favour. He could not be further from the truth.
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 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 Doctrinenote In the Legends continuity, Tarkin's line "Fear will keep the local systems in line" is not just a personal opinion but a matter of Imperial policy. 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.
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, 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—
Luke:Was my tiny mind snuffed? I must have missed that part.
In Star Wars: Kenobi, Orrin Gault, an embezzler and perpetrator of a Monster Protection Racket who's Slowly Slipping Into Evil, is repeatedly warned by Ben to "Turn back now," and can't make heads or tails of the instruction, since Ben doesn't make any moves to expose or extort him, or do anything else that would profit from the situation.
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 it is a demon, and demons are absolutely incapable of understanding what things like love even are. Therefore, there's no way it would know that Revenge by Proxy would be what hurt Michael the most. Harry turns out to be Right for the Wrong Reasons. Yes, the Nightmare is being manipulated, but it's not the ghost of a demon like Harry expected, but rather the ghost of an Evil Sorceror that Harry defeated earlier, who, as a human, could comprehend love. So it's Invoked, but not played straight.
Another Dead Beat example. Lasciel's shadow simply cannot understand why Harry wouldn't want to be like Nicodemus, and in later books can't get that Harry is quite willing to die rather than pick up her coin- which would turn him into a Fallen Hero.
In Cold Days, Mab explains her belief that Harry indoctrinated Molly into serving him: he protected her at great personal risk and indebted her to him by providing help. The reader—having had a close-up view of Harry's motivations—knows that she's wrong: he did the above because he's a good person who didn't want Molly to suffer.
In Skin Game, Hannah's prejudice against the White Council (and presumably Lasciel's manipulation) means that they never gets that Harry's offers of mercy and warnings that they're going down a dark path are genuine, and Harry really sympathizes with them and wants to help.
In The First Wives Club by Olivia Goldsmith, the Club forms when a mutual friend commits suicide due to her husband Gil leaving her for another woman. They target Gil in particular but each of the various ex-husbands have the problem of not grasping how bad they treated their wives. The ladies end up ruining a major deal Gil set up that cost his partners several hundred million dollars. When a weakened Gil asks why they're doing this, they respond "ask Cynthia" and Gil is honestly baffled what his late ex has to do with this.
Gil had planned to buy up a Japanese company than split it apart and sell it off. The girls informed the owner of this and the man thus refused to sell rather than put all his workers out of jobs. Gil's first reaction is to simply offer more money, not able to grasp someone would put the welfare of their workers over making a profit.
Explicitly pointed out in the second book when the Vord Queen that Amara, Bernard, Doroga, and their forces are fighting ends up caught by surprise and killed because, while she technically understands the concept of sacrifice, she just can't get why people would be willing to throw their lives away to prevent her threat to the rest of the world.
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 politician like himself who only pretends to be The Good Captain for PR reasons, when Tavi is 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.
In Eugene Field's Daniel and the Devil: ordinary decent businessman Daniel simply doesn't see the appeal of a life of fun and debauchery, being a respectable businessman and father of nine. 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 Dickens' David Copperfield, Uriah Heep hires Mr. Micawber as his clerk, on the assumption that paying off his debts and providing him with financial security will be enough of a vice to stop him protesting against Heep ruining the Wickfields' lives. Actually, Micawber's horrified, and uses his position to recover important documents to bring Heep down.
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.
A similar (non-murderous) exchange passes between Talos and Variel. After betraying the Red Corsairs and joining the Night Lords, Talos assumes that Variel does so out of some debt owed him from long ago. When it seems likely that the two of them are going to die in their next mission, Talos offers to 'release' Variel from his debt, to which Variel acts with outrage. It never occurs to Talos, despite all they have been through together, that Variel considers them to be friends and not just an obligation.
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.
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 rather earn the position of Clan Leader than kill the current leader and take 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 two things about the heroes in the setting: either they assume that good guys won't go out of their way to help others if they don't have to, and when they do act in a benevolent manner the bad guys think that they can be intimidated into backing down. One major part of the backstory in the books set in the Talbott Cluster is based on this misunderstanding. The Conspiracy is trying to make the Manticorans look bad by fermenting rebellions on planets in a False Flag Operation pretending to be Manticoran agents and assuring the rebels they'll have backing, setting them up to be crushed and giving the Manticorans a bad reputation. The plan assumes that if the Manticorans find out, they will refuse to get dragged into someone else's problems, especially if it puts them at odds with the Solarians, making their reputation worse. When the Manticorans do intervene, the local oppressors assume that by threatening to kill their own citizens unless the Manticorans leave will make them back off. Aivars Terekhov corrects this misconception with kinetic weapons strikes.
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.)
In Horns Lee Tourneau is utterly confused by a single line in an email from a friend two weeks after his mother's death. The line? How are you holding up? In fact, he cannot fathom compassion, selflessness or love.
Agatha H. and the Voice of the Castle: Castle Heterodyne, a mad artificial intelligence built by an even madder scientist from a line of mad scientists, all complete raving villains to a man, has no idea why the Heterodyne Boys, the closest thing to a Big Good the setting has, were never impressed despite its many, many attempts to please them. The fact that it killed their mother, a literal saint of a woman, never seems to register with it.
In his far from unbiased biography of General Moreau, Frédéric Hulot explains that Napoleon's far-reaching vendetta against Moreau stems from the fact that the selfish and ambitious Corsican could not understand why a man of Moreau's talents and influence would selflessly serve the Republic without seeking political power or personal gain.
AM, the evil A.I. of I Have No Mouth and I Must Scream is programmed unable to feel or create, but it does have creative thoughts of destruction and torture. Which it does, because it can't see humans as anything more than playthings who are utter bastards that deserve the punishments it gives them. This is expanded upon in the video game adaption, see below.
The Silerian Trilogy: Kiloran seems genuinely baffled that Baran harbors such a grudge against him over abducting and raping his wife.
In Kushiel's Legacy, the Mahrkagir serves an evilAnti-God but cannot be inducted into his priesthood, because he would be required to sacrifice someone he truly loves, and his horrific upbringing left him incapable of understanding anything but death and suffering.
It's more Bigotry Cannot Understand Good, but none of the citizens in To Kill a Mockingbird can understand why a white man would not only father children with a black woman, but acknowledge them and live with her family. He has to pretend to be a drunk for them to accept it.
There's a straight example in Bob Ewell's response to Atticus's question about what he did when he saw his daughter supposedly having been beaten and raped. He says that there was no reason to call a doctor, as her wounds weren't anything permanent- missing the point that she was hurt, and he should have cared about her well being.