The thing I started to notice was that people might seem to be asking a question, but that question is really just a proxy for another question. It's like people were communicating at two different levels.

Yep. People do communicate on multiple levels. Yes, different levels can say different things or even contradict each other. Yes, part of "social skills" is the ability to manage multiple-level communications. Yes, women are much better at that than guys. Yes, it's complicated.

:-)