The sourcebookThe Book of Vile Darkness introduced the Vashar, a subrace of coldly evil humans. The Vashar are said to literally be unable to comprehend "positive" emotions, to the point that most of them wouldn't think to use a hostage as leverage, because they don't consider that the victim's friends would care about them.
Likewise, one D&D book provided DMs with the advice that a mind flayer sorcerer might be able to predict any action the heroes would take, but couldn't see that they'd be willing to perform almost certain suicide to prevent him because he doesn't care enough about anything to risk his life. Mind flayers, like the Vashar, are said to be unable experience any emotion more positive than a sort of satisfaction during feeding. This trait is even self-perpetuating; mind flayers don't learn emotion from each other, but from resonance stones, psionic deelies that emanate a specific emotion. Because the mind flayers building these can't feel love or joy, they can't build stones that project love or joy, and as such the next generation of hideous tentacle-faced monsters won't understand love and joy either.
In Changeling: The Lost, the True Fae are utterly unable to understand human motives and rationale. This isn't just a weakness, it's a defining trait—if one does start to understand a human's viewpoint, they lose most of their powers in the process, and in some cases lose their memories of their true nature outright.
This trait is potent enough that Changelings base their own government around it. The governing of their territories is routinely passed between Courts because the Fae simply cannot comprehend the idea of mutual cooperation and the willing sharing of power, which aids in concealing Changelings from the Fae.
The Deathlords have this as one of the only weaknesses in their strategic genius. As the Abyssals splatbook puts it:
Deathlords are notoriously selfish beings, almost incapable of truly understanding others. They might, for instance, do nothing more than ascribe their own thought processes to their enemies. ("Of course you returned to rescue your sister. Doing otherwise would suggest weakness in the face of your enemies!")
And then there's the Ebon Dragon. The Ebon Dragon is bastardry incarnate. Everything it does is centered around the idea of dicking someone else over. How bad is he? He had to create the Unconquered Sun just so he'd have a concept of what he was supposed to oppose. What's more, he's explicitly incapable of comprehending the motivations behind any kind of heroism save by dismissing it as abject insanity on the part of the hero. This doesn't prevent him from preying on the "crazy heroes", because he doesn't need to understand their motivations in order to identify and manipulate their desires.
The Yozis are pretty nasty individuals and have trouble understanding that anything can operate by different rules. Their leader Malfeas has to suffer a genuine psychic fracture to understand that another being's viewpoint matters at all, and all the others are similarly limited. The Ebon Dragon knows that beings can feel positive emotions, but he doesn't understand them. He can't understand them. He will assume in any given situation that people are trying to dick everyone else over, because, well, that's what he'd do. This is simply how they work.
Most of humanity in the Warhammer 40,000 universe just want to live their lives free of war. The Orks, on the other hand, find war to be not only a bloody good time, but the only endeavor worthy of their time. To an Ork, peace is as horrible a concept as war can be to a human being. This also extends to cultural aspects, orks are naturally bald and use furry biting 'air-squigs as hair implants and use their teeth as currency, not understanding why no other species in the galaxy ever accepts these two bartering items. And since to orks, the leaders grow bigger because he's in charge and vice-versa, so it took them a while to realize the highest-ranked Imperial is not the tallest but the one with the fanciest hat and Bling of War.
While Magic: The Gathering avoids identifying any color wholly with good or evil, White and Black both appear to have this dynamic with each other when the designers write articles describing their perspective as though they were people. Black justifies its selfish amorality by claiming everyone else is just as selfish and amoral as it is and hates White for being a hypocrite (and admittedly also for White's dedication to Black's complete annihilation). White, on the other hand, believes that the morality it subscribes to is the basic nature of life and shared by the other colors despite their actions; in White's view, Black knows right from wrong in the exact same way White does and deliberately chooses to do wrong, making it irrevocably evil. Perhaps fittingly for their names, Black and White are the colors least capable of understanding others could possibly view the universe differently than they do. Things get interesting when White and Black are mixed.
Demons and devils in Ars Magica do not possess any of the Seven Heavenly Virtues and have to strain themselves even to imitate them briefly. This often takes them into Villain Ball territory: lacking Faith or Charity prevents them from cooperating even towards common goals, lacking Hope and Prudence undermines their long-term planning, and lacking Justice makes them relatively easy to lie to.