You can't separate the question word from what it refers to, in this case "mi" from "van". You have to treat them as one unit. Thus there are only two possible word orders here: "Mi van az üzletek fölött?" and "Az üzletek fölött mi van?"

Did you see boltok in a multiple-choice question, and was it a required correct option?

If so, report it - such additional words should not appear as a required option. (And az boltok is of course complete nonsense anyway.)

The course has a number of synonyms which are not taught but which are accepted (just as in English it "teaches" e.g. "pants" but usually also accepts "trousers"). But sometimes those accepted synonyms "escape" into multiple-choice questions - I think that happens when they are included as an alternative in the "best" translation rather than as a separate additional alternative translation. In which case report it.

I also got "Mi van a boltok felett?" which I assume is correct but is the first time I'm seeing either "felett" or "boltok". (I've reported it on those grounds.)

fent means “above” as in “on top”, without the “of”.

So you can say “it’s on top” (fent van) but not “it’s on top the store”.

In grammar terms, fent is an adverb, not an adposition, so you can’t use it in conjunction with a noun but only by itself.

With a noun, you need the postposition fölött instead.