Same in French, so I think it should be allowed in other sentences, but in English we are more likely to use tone of voice to make the emphasis for this question "What are you waiting for?" , but we might say "You did what?" for « Tu as fait quoi? » or we could still say "What have you done?" although we tend to say "What have you done?" which has a different emphasis. Try reporting it anyway though, you never know.
Literal translations are often not accepted though. It is much more common to say “What are you waiting for?” but yes people can say “You are waiting for what?” Duolingo cannot see the stress on the word though and ignores question marks, so usually Duolingo does not take regular sentence form as a question from English for French.
This is not actually wrong. People have been debating this for three centuries.
http://grammar.yourdictionary.com/parts-of-speech/prepositions/ending-a-sentence-with-a-preposition.html Imagine trying to put Latin rules on a Germanic language, No wonder English can be so confusing to people trying to learn the language.
There may have been more than one correct form if you were given the English to translate to a multiple choice, then “vous attendez” which is the plural form but also the formal singular form would also be correct. For multiple choice you must choose all correct answers. In French “attend” would not be used for “you”, so it was not the closest.