I like the flies. Everybody encounters them in real life from time to time, but we never see them in movies.
Facts are meaningless. You could use facts to prove anything that's even remotely true!

Found under the triva:
"The house used for filming was infested with flies, so it was nearly impossible to prevent them from appearing in several scenes. "
http://www.imdb.com/help/boards/markup

I noticed all THREE flies mentioned in these posts and was ALSO wondering the significance, if any, or if they just had a/some pesky fly/flies that wouldn't allow for a "clean" take so they left them in??? It DOES add humor to the rather tense situation (killings and all) I had to check IMDB to see if anyone else had noticed or knew the background, if any

I actually wondered if there was supposed to be some kind of deeper message or metaphor going on that I wasn't getting about the fly as there are other parts in the film where a fly played a part in a scene. Unless it was just meant to be a running gag that wasn't really particularly funny or clear.

He didn't eat it, he sucked it in from his fist and spat it out.

And don't forget the scene when The Tulip grabs the fly right out of the air and eats it. Gross, but it works with the other scenes.

There was another fly on Matthew Perry, in his face in another scene, and he waved it away. Those are real flies and they keep it in because it's real and that was the best take, plus flies are funny, to them.