I always thought the pilots created the aliens to use as a weapon. I mean, look at the thing! They're like a virus, the PERFECT organism for wiping out other species. As a weapon, they'd be unparralled. But even though the pilots created the aliens, the aliens would not serve them. The pilots kept control of the aliens while the aliens were in their ships using advanced machinery in their ships. But once the aliens left the ship, they could not be controlled, making the weapon one time use only for each ship. One pilot ship would hold a few hundred aliens.
Then something happened (I haven't thought of it yet) and the pilot ship crashed onto LV-426, which disabled the alien control field. Bye bye pilots.
I haven't thought of a reason why the ship crashed yet.