Gaston's unable to understand 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's also 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.
Shen generally has trouble comprehending that, unlike him, Po isn't the type of person to hold a grudge (or at least he tries not to hold grudges against others). Earlier in the film, he carefully rehearsed his confrontation speech, expecting Po to angrily swear vengeance for his dead parents, only for the act to fall apart when Po just casually greeted him (but to be fair, Po was very tired and out of breath at the time, and didn't realize that Shen was the one who murdered his biological family).
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."
Also, The trolls entertain True Love's Kiss as being only one of the ways to save a frozen heart, but Hans clearly believes that "True Love" can only come from the love of a man and a woman. He doesn't consider the love of siblings, though given his own relationship with his brothers and what Anna had told him about her relationship with Elsa, of course he wouldn't.
Syndrome from The Incredibles has this problem. He's blindsided when his Dragon Mirage makes a Heel–Face Turn after Syndrome left her to die to call Mr. Incredible's bluff. He never considered her feelings in the matter, so he felt that his reassurance that he knew that Mr. Incredible probably wouldn't kill her was enough. He's utterly surprised when she angrily tells him to bet his own life next time he gambles and walks away.
He also has a short moment where he completely misses the point when Bob calls him out on killing off real heroes so he could just pretend to be one. He thinks that Bob is talking about powers and disparaging Syndrome since he didn't have any, and retorted that he's "real enough to beat you." It never crosses his mind that Mr. Incredible was actually talking about morality, and meant that Syndrome was killing off good people who fought crime in order to help others so he could stage disasters and solve them for glory.
In My Little Pony: Equestria Girls, when Sunset Shimmer 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.
Abacus Cinch, the principal of Crystal Prep in My Little Pony: Equestria Girls – Friendship Games, is obsessed with winning the titular event. Once she becomes aware of the magic at Canterlot High, she assumes that they're using it to cheat, and promptly seeks to use it to ensure her victory. It never occurs to her that they would do otherwise.
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 Justice League: Crisis on Two Earths, Batman's counterpart Owlman doesn't understand why Batman doesn't come to the same conclusion about the futility of choice and thus existence.
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. Case in point: he's left utterly bewildered when Dr. Ferreiro chooses to Mercy Kill a captured rebel to spare him more Cold-Blooded Torture at Vidal's hands, despite knowing that Vidal would undoubtedly kill him for doing so.
A New Hope: Alderaan gets destroyed by Grand Moff Tarkin as a warning to star systems thinking of opposing the Empire or sympathizing with the Rebel Alliance. It has the opposite effect, making many systems more sympathetic to the Rebellion, and in the expanded universe, it even sparked a mass defection by Alderaan-born Imperial officers. Leia even told him "The more you tighten your grip, Tarkin, the more star systems will slip through your fingers..."
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 a 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.
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 Age of Extinction, Harold Attinger and the rest of Cemetery Wind are incapable of realizing that there are good and bad aliens and their actions are just as evil and extreme as the Decepticons.
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." 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... for a place like this... Why? A man like you... 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.
Operative: Madness? Have you looked at these tapes? At his face? It's love, in point of fact. Something far more dangerous.
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!
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.
Elsa Schneider in Indiana Jones and the Last Crusade. Throughout the movie, she can’t understand that Indy doesn’t want to find the grail for the same reasons as her. She insists that she “believes in the grail, not the Swastika”, but Indy retorts that she “stood up to be counted with the enemy of everything the Grail stands for.” In the end, she refuses to believe that the grail isn’t meant for her to keep. As she heads for the exit, she crosses the Great Seal and triggers the temple’s collapse. She almost falls into a chasm but Indy catches her. Instead of letting him save her, she pulls a hand free to reach the grail that she dropped. She comes so close, but her glove slips off the hand Indiana was holding and she loses her life. Henry Sr. later comments that Elsa thought the grail was “a prize” and she didn’t understand the spiritual meaning behind it.
The Devil's Advocate: John Milton Satan succeeds in the beginning because he is expert in manipulating Kevin's vanity and ego. He also thought Kevin would forget that he raped his wife and would lust after his demon half-sister. Ultimately Kevin loved his wife more and was selfless enough to kill himself rather than create the Anti-Christ, which literally makes Milton explode. And when Kevin is brought back to life, Milton sees Kevin's new moral stance as just another form of vanity he can manipulate.
At the end of Paths of Glory, General Broulard is so impressed by Colonel Dax's efforts in his battle against General Mireau to save his men from public execution that he's going to offer him Mireau's place. When Dax refuses because he wasn't doing it to have a promotion, Mireau is completely dumbfounded that anyone would try to save lives without something to gain from it, and threatens to have Dax arrested.
Midnight Run: Serrano is aggravated by the idea that someone like Jack would give up his family and career rather than become a Dirty Cop on his payroll. He also never expected that Jack would work the FBI to bring him down, instead of getting Marudukas back, which is what Jack had been focused on since the beginning of the film.
In Richie Rich Laurence Van Dough spends the movie trying to break into the Rich family vault which he naturally assumes is packed with mountains of gold, jewels, and money. When he finally does enter, all he finds is various family artifacts and memories of key moments in the Richs' lives. Van Dough is stunned, unable to accept the idea that anyone would waste a vault on such "junk," not getting that to the Riches, these are true treasures.
Van Dough: I don't get it. Where's the money?
Mr. Rich: In banks. Where else?
The Riches don't even bother hiding how they think Van Dough is an idiot for assuming that the richest family in the world would keep their wealth hidden around rather than investing it in stocks.
Green Lantern: What ultimately brings Parallax down. Because he feeds off fear, he believes courage means having no fear whatsoever. He assumes Hal Jordan will fall because he has fear in him. Courage is about not letting fear take control, which is why Parallax underestimates him and is unable to feed off him.
As in the comics, Lex Luthor has this going on twice:
In Superman: The Movie, when Ms. Teschmacher asked if he thinks that Superman is the real deal, Luthor replies that if he is, he's not from Earth. Granted, Superman is a Human Alien, but it does show that Luthor doesn't believe anyone on Earth could be as selfless as Superman.
This is his whole reason for his hatred of Superman in Batman v Superman: Dawn of Justice: he was abused as a child, and prayed to God for it to stop, only for it to continue, concluding that either God Is Evil or doesn't exist. Naturally, he views Superman's mere existence as an affront to his worldview.
In the original Miracle on 34th Street, Dr. Sawyer is about the closest thing thing we have to a legitimate villain. He openly believes that the only reason Alfred likes playing Santa, or that Kris claims to be Santa, is because they are both delusional. As far as he's concerned, anyone who's that nice has be harboring a severe guilt complex.
Munroe the Big Bad of The Expendables somehow doesn't realize that even if his operaton is making General Garza rich, the latter will still likely turn on him, after he abuducted and tortured his partner's daughter (who is a CIA informent), even after Garza made it very clear that he would not stand for that.
Garza: Sometimes, the money just isn't worth it.
Munroe: Yes it is, money is what allows people to be the real ass wipes nature intended.
Later, during Munroe's confrontation with Barney Ross, after he has taken his now dead partners daughter hostage, he tells him that they are Not So Different and he would have payed him more than whoever payed Barney to go after him "to go fishing". Barney's response:
Barney: I didn't come for you! I came for her! (Fills Munro full of lead)
The Magnificent Bastard Cipher from the Fate and the Furious (the eighth Fast and Furious film) mocks Dom for showing kindness to a cheating driver he defeated at the begginning of the film, to which Dom tells her by letting bygones be bygones, he earned the man's respect and changed him into an ally who plays a part in his scheme to turn the tables on her. This comes back to bite her in the end, after Dom makes peace with his former enemies, the Shaw brothers, he gains an edge on Cipher that she never saw coming.