As long as the question is scientifically valid, there is no problem.
Who makes the determination whether a question is 'scientifically valid'?
I don't think it's a problem for a student to ask a scientifically invalid question in class, provided it's asked in good faith. He's a student, after all, and as such isn't yet fully equipped to discern that, for example, Wells' "10 questions for your biology teacher" is loaded nonsense. If the teacher knows his stuff, it should be realtively easy to answer those ten "questions" calmly and convincingly. Answering them can also serve as a valuable opportunity to enhance student's understanding of evolutionary theory; refuting errors has pedegogical value.
On the other hand, I don't think teachers should bring up such things if not asked.