I've seen this happen twice but in a different area. It's pretty cool. The only explanation i can think of is territory disputes. In halo several factions were under the banner called the covies. Just because these guys work for the same boss and want the same thing doesn't mean they like each other. So i assume none of the factions like each other but ally under the darkness because they want to own the universe. And they can't all own everything. So they get into fights.