I find random dead flies in my house.... Can it be something in the air that is killing them?

A creature may have died in a hidden place, perhaps a mouse inside a wall or a bird in the attic, etc.; or you may have dropped a piece of food in a place you can't see; or you haven't taken the garbage out often enough. Flies are attracted by rotting food and flesh. They can smell it from long distances. If it were a long standing problem, I would guess that there are gaps around your Windows, doors or just about any place around the dwelling.