The finite verb does go to initial position but sometimes Duolingo wants the word order of the original sentence. The "normal" English question would be "Do you have a father?" Since the "you" is in initial position, they might want "Du" in initial position as well.
Akkusative! It is useful to ask a question: Wen hast du? (Who do you have? Ich habe einen Vater (I have a father). This doesn't change when the sentences changes to a question: "Hast du einen Vater?" Hope this helps.