Well Josh, the key lies in knowing how to translate certain things. For example, "be honest with me" really means "tell me what I want to hear." And "we haven't resolved this yet" really means "I have not won yet." It took me a very long time to figure this out. Of course, now that I have figured it out, I do not use the knowledge, rather I avoid those types of women. There are good women, and so I look for those.
I'd recommend reading the Mars and Venus book--it's great for normal misunderstandings.
For misunderstandings that seem like they come from the twilight zone, read up on Borderline Personality Disorder--75% of those who have it are women, and it will explain the actions of LOTS of women that you have met, trust me. Read "I hate you, don't leave me" or "stop walking on eggshells"--those are two good books on the subject.
I think a lot of women get themselves into trouble because they want certain things from men and handle it wrong. Like for example, if they want to be told a certain thing affirming the relationship. But the man doesn't say it that day or that week or whatever. So the woman asks him a bunch of questions getting him to say it, then when he says it she really knows it was only because she 'manufactured' the response. So she doesn't believe him. When he sees she doens't believe him, then he feels like he can't win because she tried to get something, he gave it to her, and she rejected it.