The English translation is definitely awkward. "Who is eating my banana" or "who ate my banana" is correct. Ben when was the last time YOU said "who eats my banana"? If someone is eating it now, you'd know about it.
In English we would ask, "Who ate my banana?" or are you meaning, "Are you eating my banana?" The English translation is awkward - in Hebrew are you suggesting someone ate it and the person wants to know who? (past tense) Mary Jane