Last Spring, I suddenly has a fly problem in my house. Apparently, a couple of flies got in my house and mated. Suddenly, there were flies on every window. I personally flushed 50 of them down the toilet in the course of two days.

Finally, I got some flying insect spray. I watched the flies to see where else they would land besides my windows. By studying their behavior, I found the "nest" (if there is such a thing) in a high recessed light fixture. I sprayed it well with insect spray. That solved the problem.

Nowadays, I kill any fly that comes into my house as quickly as possible. I had no idea that flies could mate and duplicate inside your home. Perhaps this is what is happening to you.

Another suggestion: check all your screens, screen doors, etc for holes. Have them patched. Don't keep doors or windows open unless they are properly screened.

Good luck.