"Vous etes qui" means "who are you". "Vous etes Mme Lupin" means "You are Mrs Lupin". How is that, I'm confused? I've only been studying two weeks!

As for "Vous êtes qui?", I don't know what this kind of question is called. It's not an est-ce question or an inversion question, but it's fairly typical. Pronoun--verb--question word.

That's just the syntax of French is this case. Maybe it helps you to think of "Vous êtes qui?" as "You are who?"

Actually "Vous êtes Mme Lupin", could be a question as well. You would simply have to raise your voice at the end of the sentence to make it one or place a question mark behind it when writing. We sometimes do this in English. For example, if someone tells you something that seems surprising you might say "It is?" or "You do?"

There are other types of questions, but I won't get into them as you just started learning French two weeks ago.

I hope this helps.