If there is a fixable problem with a question and somebody hasn't already commented about it, leaving a comment asking for clarification or otherwise explaining the problem is a good thing. To forestall discussion in comments you can add something like "Please  to add details" (or whatever the issue was). Try to avoid conversation in comments, but please don't avoid commenting at all and surprising the user -- and anybody who was working on an answer -- with a closure later.
Another answer says that flagging means you want something deleted. That's true for many flags, but users who can't vote to close can flag to close, and close means close, not delete. (A question that stays closed could get deleted later, but the point is to hit "pause", fix the problems, and reopen.) A close flag usually sends the question to the close-votes review queue.