I guess... Duolinguo should start making a difference between thou and ye in the context of different languages... I mean... ¡Almost every language in the planet has a distinction between plural and singular "you"!
You can't expect Duolingo to actually use thee/thou/thine as English words, because this would mis-lead people who are learning English as a foreign language. English does not use that form any more - we only use plural/formal you.
It is correct, and it's also put correctly on the list of answers, so it shouldn't give such a highlight... perhaps something else was wrong? The grading algorithm has problems with showing what exactly was wrong.
It's not unknown for Duo to highlight the wrong thing as a typo. If you have no actual wrongly spelled words, but you get the word order wrong, that can trigger typo reports on one of more of the correct words.
I'd say that "have you used" is quite clearly perfective and "were you using" is clearly imperfective (so I agree that "użyłeś" doesn't work here). "Did you use" is rather ambiguous, it can cover both aspects.