Fuiste is the second-person past for both Ser "to be" and Ir "to go." When talking about location, however, we use Estar, not Ser. Tú estás en la clase. Maybe try translating it from past to present first - think about "Tú no eres a la clase" and "Tú no vas a la clase." The first is wrong and the second is right, so "No fuiste" must be "You did not go", not "You were not" in this particular sentence.
For me this is the hardest thing about past tense. I get it wrong all the time.
That seems correct to me, especially since my "You did not go to class" was marked as correct (Feb 11 2104). I hope you reported this. Or maybe it's been fixed since you posted this comment. Duo is usually pretty good about accepting "do not" and "don't" interchangeably.