It's because of where you're setting the bar. To stop being fruit flies, a population would have to speciate, genus-ate, and then family-ate.
common name for any of the flies of the families Tephritidae and Drosophilidae.It might have to actually go a taxon higher than that (order), since the term "fruit fly" encompasses two families now. Speciations have been observed. That's more than what creationists usually admit as possible.
I'm setting the bar too high? So? What's wrong with the concept of a fruit fly turning into a fish over thousands and thousands of generations? Isn't that exactly what millions of other animals are supposed to have done on their own?