Flies or moths??
If they are flies, they are more than likely coming in from a window or crack some where. It's happened to me before. I'd come home and there were tons of them at the kitchen windows, and it freaked me out. A few of my windows, when I had them up so the screens let in air, would slide down at the top and let in flies. Another time they came up from the basement (unfinished and just creepy) and would hover around the kitchen windows.
If they are small moths, then they come from boxes foods. And those are an entirely different story to get rid of.
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