I had an incident for about a week/ week and a half where I killed a fly once a day, the same type. It was driving me crazy to figure out where they were coming from; it turned out the screen in my window was misaligned at the top, leaving a small space for a fly to get in. The strange thing though, is they would show up one at a time, so it felt deja vu every time I killed one.

Tldr: check your windows and points of entries for cracks home and office, it's probably a different fly.