I hate fruit flies! I don't think it's b/c of the vinegar - I would put your fruit away for a while, though. We had an issue with them for a few days. ick! What happened, is that my 3 yo threw a banana peel away upstairs in my oldest DS's trash can in his room. It's always only held papers that my kid cuts up while doing projects, so it hadn't been emptied in at least a week. Anyhow, we realized that was the source. ugh!
What I did to get rid of them is set a trap. I filled a glass about halfway with water, and adding a splash of apple cider vinegar (b/c they do like that, maybe it's the apple in it?), and a squirt of dish soap. I put a piece of saran wrap on top with a rubber band and poked a few holes with a fork. The fruit flies went into the holes, and b/c of the soap they couldn't get out of the water. I caught a lot (uh, way more than I thought we had flying around), but it was fast, and the problem was gone overnight after doing this. My DS even added a piece of cantelope saying it would attract them faster. LOL! But they were gone afterwards. Nasty things. All they need is a little bit of water to multiply, even in the drain - so run your garbage disposal and pour hot water down it.
I clean with vinegar all the time - and have for years - so I don't think that's the culprit. If you find a source, like I did, that's the biggest part in eliminating them. Then you have to trap the rest.