I just saw this thread.
I don't see any defensiveness in the way you respond. It seems like the logic part of your brain points out to you that the question could be taken two ways.
I do this myself sometimes and there have been times when it has led to awkwardness.
I think saying "I don't know" is by far the best option if you 1) either can't quickly decide what the person really means or if 2) the person has phrased their question awkwardly enough that there really is no way to tell what they mean. (And speaking of awkward, that sentence was.)
I've decided that "I don't know" or "I'm not sure" is the best response after saying "I don't understand" several times and getting a defensive response.
I'm sorry to say that I don't know the name for this particular phenomenon. My impression from inside my own head is that it may have something to do with processing speed. It's like my brain slows down for a split second when it realizes that two meanings are possible.
My brain doesn't do this all the time, and it seems to crop up less often the older I get. I'm happy about that, because as you said, it requires a lot of work trying to figure out what people meant. (I think you said that; I can only see the last two lines of your post on my screen and I'm too lazy to scroll back to confirm.)