Hmmm... this is a tricky one. We would rarely ask in that way. It all depends on the context, you have to use your judgement. I think normally we would guess the reason, and try to confirm e.g.
"What, don't you agree with me?"
"Sorry, did I just upset you?"
If they are deep in thought, you might say something like:
"I can see the cogs turning."
With the idea you might snap them out of a daze and they might start to explain what they are thinking.
Or maybe they just don't have anything to say right now and you should just continue talking. If you feel that maybe it's just not an interesting subject for them, then you can switch to some other topic.