"Uh...stupid question?" is a fairly common way of introducing a question that doesn't seem to have been addressed, but to which everyone else seems to take the answer for granted. It doesn't presuppose the correctness of the material being questioned. It's a diplomatic way of saying "either you've not explained this properly, or I've missed something".

I would rather keep it as "stupid questions" (a known turn of phrase referring to this specific circumstance, which is how it's used), rather than something more awkward yet marginally less ambiguous.