The drain flies are really obnoxious this time of year.

They even lay eggs in my filtered cat water bowl. A poopy water dish is heaven for them. I just had to tear down a hatchling tub because of that. I didn't know how many crawled out into the bedding. =\

You can always grab a sample from them next time and ask the vet to run a fecal test. A lot of vets will run the test whenever you bring poop by, but if there Iis a positive result they'll need to see your pet for an exam before the prescribed any medicine.