The Bad Guys (2022): This ends up being a problem for the titular gang, who are trying to fake their reformation to avoid a jail sentence. They are so used to committing crimes that the very concept of doing a good deed is foreign to them, and their attempt to rescue the guinea pigs from Sunnyside goes so badly it almost lands them in jail. They gradually grow out of this once they reform for real.
Cats Don't Dance: Considering that she was confident that she had crushed Danny's hopes of achieving his dream, Darla was completely baffled that Danny would still continue fighting for his dream and would later turn the tables on her during the climax song. His Batman Gambit is what eventually leads to her Villainous Breakdown.
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 his Alpha's control to protect Hiccup. Since Drago's dragon army has no loyalty to Drago himself, they are quick to side with Toothless and help him chase off Drago and his Bewilderbeast.
In How to Train Your Dragon: The Hidden World, Grimmel believes that humans are superior to dragons and that Hiccup's desire to live among them as equals is an aberration that could doom mankind. That and he's a hunter that delights in hunting dragons, Night Furies being his #1 priority should any be found. This is soon proven to be his downfall, Hiccup's life being saved by the Light Fury after he frees her from Grimmel's control to save Toothless (performing a Heroic Sacrifice in the process) while Grimmel plummets to his death, the dragons he had enslaved all either drowned (due to being chained to his transportation harness) or having fled.
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.
Kung Fu Panda: Tai Lung's arrogance prevents him from understanding that the secret to limitless power lies not within the Dragon Scroll, but within himself, hence why he's totally unable to understand the Dragon Scroll's wisdom. If there is no secret he's been fighting for, after all, he's been destroying everything he once loved for nothing. Word of God says this is the only thing that prevents him from making a Heel–Face Turn. Also a tragic one since it emphasizes how he needs external validation of self-worth, both because of Shifu's expectation (Tai Lung pretty much means "dragon warrior") and the influence of the setting (in Asia, especially in older times, there was a great deal of the importance of lineages and where you came... which meant orphans or adoptees like Tai Lung tend to develop issues.)
Kung Fu Panda 2: Instead of questioning how Po grabbed the cannonballs and threw 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 advice that he should not let the past control him.
Shen generally has trouble comprehending that, unlike him, Po (for the most part) isn't the type of person to hold a grudge. 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).
Kung Fu Panda 3: Kai cannot comprehend why Oogway turned on him and sealed him away, despite the atrocities he's committed.
In a more subtle way than the previous villains: Kai has no idea what to make of Po when he becomes a true Chi Master by coming to a realization of who he really is. Kai never reached enlightenment like Oogway did and his control over chi comes from stealing it, so the sheer power Po had from his realization and having Chi shared with him by his friends is something Kai can't understand.
Lucky and Zorba: During his song Big Rat declares victory because he believes all the cats have gone crazy, as it's the only reason he can think of that the cats would hatch and raise Lucky, a bird.
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.
Shrek 2: Fairy Godmother wants nothing more than to have dominion over Far Far Away and has no issues using others to get this, including her son, who's she's groomed his whole life to marry Fiona and become king of Far Far Away. So she is confused why Harold feels bad that Fiona doesn't love Charming and simply gives him a potion she made and threatens him to give it to her.
Bowser from The Super Mario Bros. Movie doesn’t seem to understand that repeatedly threatening Peach’s kingdom, trying to kill the guy she enlisted to stop Bowser, forcing her to accept his proposal to marry him, and wanting to kill several innocent people, including the captured Kongs and Luigi, as a wedding gift is not the way to win her heart.
