I put "Don't waste food." Which is the basic meaning and the more common way of saying it in English. Unless they add more context there is no way they can assume the answer the Duo lingo portrays as the right answer. Some things don't translate exactly and in this situation in English with this context, it would not be said this way in English. They need to add a little more context.
Maybe not because leaving food does not necessarily mean wasting it. In most instances it can be implied, sure, but what's here is the literal translation. 남기다 can also mean save or set aside. A somewhat awkward phrase indeed, but you could be talking about not saving/setting aside too much food for someone else or yourself later.