If I have a question, even if it seems silly, I'll usually ask it. I think with NTs, we see so many sides or possibilities of interpretation, that it's better to clarify that we're on the same page as the person who's talking. Just to make sure we're not off on some completely different thing.
I sometimes, as CC mentioned, will ask a question just to make someone think about what they're claiming a little more. Because it's easier and less conflict-inducing than saying, "Idiot! That makes no sense!"
In college, I would sometimes ask questions if I felt like the teacher wasn't being clear, even if I could still follow what they were talking about. I did that because I've never minded asking questions, and most people are too shy or embarrassed to ask, even if they're really confused.