Should I email my professor to clear up a (possibly very irrelevant) awkward misunderstanding? I’m doing my master’s and I recently had an exam with one of my favorite professors. 
I spent a lot of time on my paper and got the highest grade and I’m very happy. But during the oral part of my exam, when I was supposed to defend my paper, the professor pointed out I haven’t referenced much literature he mentioned in class and asked if I found anything of the reading material he gave us interesting. I was very tired and nervous and sort of ignored the question/moved on to another subject. I later sort of indirectly asked him to be my thesis advisor because I’d like to do my thesis on a similar topic to the one I did my term paper for his class on, and he said another professor would be better suited (I don’t think that’s necessarily true).

The truth is I reaaally enjoyed all of his classes and found absolutely everything interesting and I really wanted him to be my advisor, but I think he got the wrong idea. Would it be crazy to email him and say I feel weird about the way I dodged his question and explain the situation? I feel like I gave the wrong impression, and that might be why he rejected me. On the other hand, I don’t want to look like a complete weirdo for still thinking about this (it’s been three days), and I think he might have went on vacation and I don’t want to bother him with this because it might all be in my head. What’s the right thing to do?

TL;DR: A professor I really like said he wouldn’t be my thesis advisor, and I think it might be because I didn’t answer his question when he asked if I found his class interesting. But I very much do. Should I email him about it?
If I were you, feeling uneasy about your previous conversation, I'd stop by during your professor's office hours rather than sending an email to express your concern.  It's more personal.  Pick a time when he appears free.  Tell him you've been feeling bad that you may have given him the wrong impression, that you want to make clear that you really like the class and really did find the readings helpful.  It's pretty likely he'll set your mind at ease, reassuring you that he didn't take offense and wasn't upset but appreciates your stopping by to discuss.