A question asks two different things, Q1 and Q2, and both things have been answered already. What is the proper way to flag this question?
You need to make an educated guess. Take the 'most important' (probably defined as the one that's going to take the OP furthest forward while leaving the other as a continuation to follow up) and vote for that, then comment to the OP suggesting they follow the guidelines and ask distinct individual questions (obviously providing the link to the subsequent potential duplicate for reference).
It might be that if the user has happened to ask two or more questions then they're flaunting their ignorance and would never 'play fair' - in that case it might be more appropriate to vote to close.
Bottom line, it depends.
One fairly common solution is to flag (vote to close) the question as a duplicate of one question, then also leave a comment that the offending question is also a duplicate of "this other question". In the end you should end up with two comments pointing to two questions as possible duplicates.
