No reason - it should be accepted. As well as "I had been waiting for you" and simply "I waited for you". Report it.
Russian has only only one past tense, so it makes no distinction between these English tenses. A context takes care of the precise meaning.
Do you think it should be something else?
Accusative is used for animate things after ждать (according to discussions in other exercises).
That's right. Furthermore, even if you decided to go for genitive (which you should not in this example, but that's the other case possible with "ждать"), you'll get the same sentence as the genitive and accusative forms of Вы coincide.
I waited for you not accepted today. I'll report since it has not been corrected.