Fly's will be in Freeplay Mode and will eat dead corpses. They may not seem that bad but you must keep their population down. If you don't they will breed and breed and they can be dangerous to the colony. When something is killed and when there's a high fly population, tons of fly's will start to swarm and rapidly eat all of the food from the dead insect or fish. If this happens you will have barely any food to feed your colony. So you should try to kill as many flies as you can. They only give you 2 food per fly though so you really can farm them.