Greetings - Although I don't have a solid solution for fruit flys, I might share with you what we have done. That is basically limiting, to two hours, the amount of time fresh fruits and veggies are out. We used to keep them in the cages all day, but then ran into the same problem you are having...lots of pesky little buggers hovering around. Other than that, no magic wand that we know of.
Below are the solutions from Macaw Chat for fruit flies. Best wishes! Bill
I use apple cider vinegar with a few drops of dish soap in it. The vinegar attracts the flies and the soap kills them. I just bought a couple of votive candle holders from the dollar store, pour in some vinegar and a few drops of soap. Set them around the house. It really works for me.
The lengthy one is to use a wine bottle with a little wine left in the bottom of it and leave it on the counter. The flies go in and have a hard time finding their way out. I don't drink wine, so I use a soda bottle and put some cheap balsamic vinegar in the bottle and then shake it so it is very aromatic and leave that on the counter. I check it often and when I see flies in it, I put the cap on the bottle and shake it to drown them and then take the cap off again and keep repeating the process over and over until the flies are gone.
The quicker solution I use, when I am really annoyed with them, is that I leave a lighter on the counter, with the flame set on the highest setting. I put some lure on the counter that will attract them and then I go after the flies with that. But you have to be careful with this method.