Happens every year.  No matter what you do they come.  The dreaded fruit flies.  What to do?  My husband showed me a great trick a few years ago.  And it works like a charm.

All you have to do is put some apple cider vinegar into a small bowl.  Stretch cling film over it and poke holes in it.  Make sure the holes are just big enough for them to get in.  They are attracted by the smell and then they drown in the cider.  It works quickly.  Just change as needed every couple of days until they are gone.