"Sir, do you drink wine?"
Translation:Señor, ¿usted bebe vino?
When you address someone as "sir" or "ma'am," you are indicating that your relationship with them is formal. Your sentence will continue to reflect that relationship by using the formal "you" (usted).
You could use ¿bebes vino?" with someone you're on a first-name basis with, a friend, someone your age, etc.
Marcy is correct about the formal 'bebe' of course but this addresses your actual question which seems to be about dropping 'usted' - it does clarify that the question is addressed to the Señor, since bebe could mean Sir, does he (or she) drink wine? The usted removes the ambiguity. Of course, in real conversation, the meaning would ne obvious in context.
"Senor, bebe vino usted? " <-- was marked wrong. I thought the subject/verb word order was flexible in Spanish. I assume my answer is wrong, but wanted confirmation, since Duo has been wrong before. Thanks!