Most of the times I have fruit fly problems, it's turned out that a small potato has escaped, rolled behind something else, and expired quietly.

I have memories that are fond now, but not-so-fond at the time of our pantry when we lived in Tanzania when I was a kid. We'd buy a stalk of bananas when the truck came through and hang it up in the pantry, and it would be surrounded by a cloud of fruit flies until we'd eaten them all.