Where do flies originally come from?

They are thought to have originated in the southern Palearctic region, particularly the Middle East. Because of their close, commensal relationship with humans, they probably owe their worldwide dispersal to co-migration with humans.

Do flies come from poop?

They have unhygienic breeding habits

House flies will lay their eggs on items such as feces, rotting carcasses, and decaying fruit. Why is this? Well, it's mainly to provide the larvae (maggots) with something to eat when they hatch.