One piece of advice I've heard for characters with false beliefs or misunderstandings is that each character should be the the hero of his or her own story. In other words, a character shouldn't do bad things because the character wants to be bad, but rather the character acts because the character believes something to be right. Many times, it is the character who disagrees with mainstream beliefs in some manner who is the heroic character.
Perhaps a person may believe in scarcity of something; a medicine, food, water, or some other resource. Because of that belief, the person might believe rationing to those most deserving is justified for the benefit of all mankind. This could justify subjugation of those the person felt were undeserving. The person could take very bad actions for what the character believes is a very good reason.
A person with a background in being suppressed might fear the arrival of an advanced alien race. That person might actively lead attacks against the aliens to protect humankind even if the truth is that the aliens are benevolent.
A person may believe that a passive, yet intelligent species is not strong enough to protect itself. The person may feel justified in controlling the species 'for their own good.'
One thing that I have found that helps me is to write a backstory for significant characters to explain why they act they way they do. This may be as short as a couple of lines or it could be a past incident that runs to several pages. This text never appears in the story, but helps me understand the motivation behind a character that causes him or her to act as they do. It also helps me understand the actions that the character does not take.
Does this sort of address your question?