Because Duo is trying to force you to recognize the question, but it doesn't pay attention to punctuation.
Not sure why a native speaker would be checking issues related to these lessons - but does anyone have any insight as to whether this woman's pronunciation is any good? I frequently can't understand subtle differences in her speech, whereas I speak with Brazilians and have more success.
how can I differentiate from "Você ama minha irmã" as an affirmative statement from a question?
If it is written, you can look at the punctuation. If it is spoken, you can listen to the intonation.
Is it just me or the audio partially skips the word minha? It sounds like "Você ama m...irmã?"
Why is it 'ama' and not 'amo'? Is it because the loved one is female or is it because the lover is female?
Because ama is the third person singular conjugation for amar. Você is a third person singular pronoun having nothing to do with the gender of the subject (the lover) nor the object (the one being loved)