A good example is how we tell people they're being rude. Many nerds want an explicit, clear answer, maybe even a right/wrong mark or a grade. In reality, we respond to body language with body language. If everyone's avoiding your eyes or shooting you dirty looks, you've probably said a bad word. Sometimes it's more subtle, such as with the many meanings of crossed arms and angled stances.
I dealt with these challenges by studying acting. The practice of theater collects and refines centuries of study in body language, emotion and personal interaction. Even more importantly, it is a practice rather than a knowledge base, which matters if one believes that one physically cannot learn certain things from a book.