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- Atomic Robo: The villain ALAN is an artificial intelligence built by Alan Turing during World War II that was subsequently abandoned (not by Turing's choice, mind you; The military wasn't aware of ALAN when they fired Turing, thus preventing him from accessing the base the AI was stored at) for decades with nothing but his primary objective of gathering knowledge. To this end, ALAN manipulated things behind the scenes to keep the cold war going, so he could collect enough nuclear weapons to build an Orion Drive and leave earth behind. When Robo hears this, he angrily points out that ALAN could have ended the cold war earlier, and used his immense knowledge to help humanity.ALAN: I don't understand. Why?
- Berrybrook Middle School: James scoffs when he hears Garrett confessing to Jorge. He threatens Garrett to not tell and gloats to Jorge that if he tells the truth, Garrett gets everyone's scorn instead. The idiot doesn't consider that Jorge's friends would find out it was Garrett and defend him to the student body, or that Garrett would be brave enough to confess to the principal.
- Bigfoot Bill: In the first book, Mothman has the ability to look into the future and foresees a "terrible" gate that will be built by friendship. However, because he doesn’t understand the concept of friendship, he can’t see where and when it will happen. He’s especially perplexed by the fact the Bigfoot Bill is friends with Agent Beckner, of all people, or species for that matter.
- Bitch Planet: Overweight and sardonic Penelope is being "tested" by the ruthless prison wardens by being forced to look into a mirror that shows her what her true ideal self is. The wardens believe this will "help" Penelope by showing her as what they think is the ideal woman (thin, beautiful and sedate). Resistant at first, Penelope looks into the mirror... and it's her own reflection. The wardens are baffled, convinced the device must be malfunctioning, unable to understand why an overweight and unattractive woman would be happy with that appearance.
- Disney Ducks Comic Universe:
- A Letter from Home: Molay's first assumption, when he sees a subdued Scrooge leave the clan cemetery, is not that he was mourning for his parents but that he failed to find a clue he was looking for.
- DuckTales: In the "Scrooge's Quest" arc, Scrooge exploits this to get the upper hand on Glomgold again after his enemy has managed to take over the city in his absence. He wanders around, doing everyday activities and periodically noting that a particular time has come around again. Glomgold goes crazy trying to figure out what sabotage Scrooge is perpetrating, and Scrooge is able to work this into getting everything back the way it was. He explains to the triplets, "Glomgold is so evil and sneaky that he thinks everyone is as evil and sneaky as he is", so he drove himself crazy thinking of all the things he'd do to Scrooge if their positions were switched.
- Paperinik New Adventures: The Evronians have a similar characteristic: in spite of being Emotion Eaters, the vast majority of them don't actually understand the power of emotions outside of food for themselves, nor have a large emotional ability to feel them. This proves to be the undoing of more than a few of them, who either don't anticipate someone else's reaction to their otherwise good plans or lack the emotional self-control necessary for some thing... and makes the few who can that more dangerous, as they come as a genuine surprise. Or, in one even more surprising case, a genuinely good person.
- East of West: This is Archibald Chamberlain's Fatal Flaw; despite being a brilliant and cunning man, he just can't seem to get out of his hyper-cynical mindset where almost everyone is as selfishly ruthless as him, and the few genuine do-gooders are idiots. It ultimately leads to his death when he ends up in a Mexican Standoff with Solomon and the Ranger. He expects them both to do the pragmatic thing (Solomon to shoot Ranger since he's a threat to both, Ranger to capitalize on Solomon's injuries to shoot him), allowing him to kill the remaining shooter. Instead, they both shoot Chamberlain; Solomon because it's the morally right thing to do (even if it will lead to his death), the Ranger because he swore to kill Solomon last and he keeps his promises no matter what.
- Empowered: In Volume 2, 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.
- Hound: As the goddess of war, Morrigan detests concepts like peace and mercy. It is best seen near the climax of the story when she says it's shameful of Cú Cullan to spare Queen Maeve and stop both sides of the war from fighting any further.
- Irredeemable:
- The Plutonian doesn't actually understand good and never did. The reason he was The Cape for so long was because of a deep pathological need for mindless adoration brought on by his shitty childhood. He was never actually interested in justice or being good, he just mimicked these actions to get the approval he craved.
- In Incorruptible, this is at least part of the reason that Max Damage is having trouble performing a Heel–Face Turn, despite the fact that he honestly wants to be The Atoner. He still has a "villain" mentality and either has little idea what to do other then the opposite of what he would as a criminal or does things that no proper superhero would in the name of getting the job done, like killing villains or encouraging angry mobs to take vengeance on criminals.
- In Jason vs. Leatherface, it is stated that Jason Voorhees has been pushing on for years with his feelings of hate and anger. When he finds himself sympathizing with Leatherface, he is utterly confused.
- Lucky Luke: The Bounty Hunter: The title character cannot comprehend why Luke prioritizes justice over money.
- The Simpsons: In one issue, Lisa tries selling seeds, only to be told by Mr. Burns to stop since he's an Enemy to All Living Things. When Springfield gathers together to have a seed fair anyway, Burns is confused. Smithers suggests that maybe the people of Springfield have learned to work together to overcome a mutual obstacle. Burns considers this for a moment, then decides they're just being impudent.
- Sonic the Hedgehog (Archie Comics): 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).
- Star Wars Legends:
- Star Wars: Invasion: A recurring theme in the comic is that the Vong, who are raised in a merciless Proud Warrior Race culture, have a difficult time grasping ideas like mercy or valuing lives for reasons other than cold pragmatism. Tsalok cannot for the life of him understand why Finn didn't kill him when he had him at his mercy, and the Vong outpost on Dibrook later has a difficult time working out why a large Republic force has entered a hostile environment to storm an enemy fortress just to rescue malnourished, unarmed civilians who can't possibly be of use to them in the war. A Vong Shaper compares this to another puzzling incident earlier when their prisoners rose up in a hopeless revolt when the Shapers started experiment on a captive child.
- 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, light or dark. 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.
- Valhalla: Although an Unsympathetic Comedy Protagonist rather than an outright villain, Loki, being the god of lies, deceit and politicians, is a fundamentally dishonest person and can't really grasp the concept of being honest and truthful. To him, everyone lies all the time and cloak their real agendas in pretty words. Heimdall gets a rise out of him in "Freya's Necklace" when he asks him what he could possibly know about honesty.
