The translation I was given was "Where will the money come from?". The answer I gave was the slightly awkward "From where will the money have come?".
Even if I rewrite my sentence to better match theirs: "Where will the money have come from?", it still asks a different question and I believe Duolingo's version is wrong.
Well, the idea that "prepositions at the end of sentences" were to be avoided was introduced by essayist John Dryden and became part of 18th c. Grammar books...and has been discounted ever since. English is not a Latin-based language, so there is no problem with prepositions at the end of sentences. Placing prepositions at the beginning of a question that starts with a "wh" interrogative adverb results in an awkward-sounding construction.