At one point, Ultron-6 rebuilds himself with indestructible Adamantium, making him invulnerable to anything that the Avengers can throw at him, including Thor. Ultimately, Hank Pym stops Ultron via Logic Bomb by impersonating Ultron's Mind Probe target after undergoing hypnosis to fill his mind with a simple phrase that Ultron's robotic Kill All Humans mindset can't understand: Thou Shalt Not Kill.
Doctor Spectrum (one of the villainous ones, not the Squadron Supreme member) once attempted to prevent the Avengers from defeating him by first disposing of Iron Man (who had previously fought Spectrum and discovered his vulnerability to ultraviolet light). The Avengers still used this to beat him, Spectrum screaming "No! Only Iron Man knows!" as he fell unconscious — the Vision then remarks how foolish Spectrum was to not realize that of course Iron Man told his teammates, while Spectrum had assumed that his foe wouldn't give up the "advantage" of being the only one to know a certain enemy's weakness.
During The Terminatrix Objective, a future version of Ravonna abducts several versions of herself, mostly villainous versions, to show a version of her who has decided to live out her life with Immortus, and prove that they (Terminatrix especially) have become so warped that this would be impossible for them.
Doctor Doom gets hit with this in the storyline where he saves Reed and Sue's second child. His price is that the baby girl must be named after his lost love, Valeria. Doom, a hardcore egotist with a compulsive need to be the best, thinks that this reminder of inferiority will constantly grind away at Reed. Reed, for his part, doesn't give a crap, and is simply happy that his daughter is alive.
Doom gets hit with this again in Grant Morrison's mini-series "1-2-3-4", when he attempts to use an alien computer called the Prime Mover to play a four-dimensional chess game against Reed, thinking that he can destroy the team's familial bonds. The key to Reed's outplaying Doom lies in that family connection:
"My family are an equation. Alter one part of the equation and it no longer tells the truth. You failed from the start. You can no more change our essential nature than you can change E=MC2."
A key reason why the Mad Thinker is constantly defeated is because, despite all his genius and amazing ability to predict things in advance, he still fails to calculate how people will react differently than he expects them to in non-selfish ways. He even lampshades it at times with how things like empathy and self-sacrifice create a "margin of error" in his plans.
The Incredible Hulk: In issue #165, "To Become a God", Mad Scientist Captain Omen is dumbfounded to learn that his son is the leader of a rebellion amongst the mutant children of his mobile deep-sea colony and asks what could have possibly turned his son against his father's mission to map the sea floor and claim it as his own sovereign nation. After all, he muses, his son would have inherited dominion over that nation, and everyone wants power! It never occurs to him that his son might resent having been born into Omen's mad mission and kept sequestered from the surface for his entire life... especially since Omen never mentioned that the deep-born mutants can't survive out of the sea's depths.
The Mighty Thor: While living in Midgard against his father Odin's wishes, Thor falls in love with a mortal woman named Erika. Loki convinces Odin to let him continue with his romance, until Thor is called away to intervene in a war between realms. When he returns, he finds that he has been away a lot longer than he realized, and Erika has passed away from old age waiting for him. Loki is certain that this heartbreak will be enough to drive Thor to return home to Asgard. However, to Loki's astonishment and Odin's infuriation, the experience has only deepened Thor's love for Midgard, and he stays there to celebrate Erika's memory.
Loki:Why, brother? Loving them will only ever bring you pain and suffering. More than even I ever could. It's almost as if... Heh. Loki isn't your greatest enemy after all. And never will be. No... it's Midgard.
The criminals targeted by The Punisher are forever yelling at him that killing them won't bring his family back or impact crime in any way. It never occurs to them that Frank is perfectly aware of this and that he has simply devoted his life to killing scum until he dies.
In the "Six Hours to Kill" arc from The Punisher MAX, he's poisoned by Baltimore criminals who want to use him as their own attack dog. He kills the guy who injected him and spends the next few hours killing criminals as usual (and because Baltimore isn't his usual turf, quickly goes through those on his list)... and is actually disappointed when one of his captors injects him with the antidote with seconds to spare.
One would-be baddie tries to rattle the Punisher by sending out people who are surgically altered to look like the Punisher's past victims. He believes that this will shake up Frank and that he's constantly haunted by the nightmares of faces he's killed. When he confronts the man, Frank points out the key problem with this entire plan:
Punisher: What makes you think I'm haunted? I send them to hell. I sleep just fine.
During the Amazing Spider-Man tie-in to Secret Empire, Doctor Octopus attempts to reclaim Parker Industries from Peter, only to watch in horror as Peter destroys his company to keep it out of his hands. Doc Ock yells out asking why someone could be so unbelievably petty to do such a thing, but Peter tosses it right back, telling him that a man would willingly lose everything to protect people.
In Strange (2022), Clea is frustrated and outraged when she learns that her mother thinks her marriage to Stephen Strange was all part of a long-term plan to take his role as Sorcerer Supreme, rather than consider that Clea genuinely loved him.
In an Avengers/X-Men crossover, Magneto develops a helmet to alter human minds, thinking that it's a great way to unite the world. Captain America tells him that this is wrong, and Magneto uses the helmet to remove any anti-mutant feeling from Cap's mind, assuming that this will sway him. When Cap says that he still feels the same, a stunned Magneto confesses that he always assumed that every human had a hate of mutants in them. The realization that Cap truly feels this way rocks him enough to destroy the helmet and surrender himself.
It's clear that many of the anti-mutant bigots who push the idea that "mutants want to destroy us" are unable to accept that A) not all mutants are alike and B) that people with power would want to live a normal life and not use that power to oppress others, because they themselves would abuse their powers if they had any.
Stryfe sets up a trap for Cyclops and Jean Grey where they find a child (really a robot) tied to a computer system and he tells them that killing the child will kill Stryfe. At the time, Stryfe believed that he was the child that Cyclops once abandoned and thus totally believes that they'll do it. He's literally shocked speechless when instead, the duo fights the massive number of robots that Stryfe sends after him, and the caption boxes note how his entire worldview is being shattered.
