I may be slow in saying this - I did a brief search in the forum to check for repeats so hopefully I'm not being an idiot here. One great piece of realism in the orbital set up in the current patch: 58772, is that the orbital pods used to launch units built by the factory will cause damage to units that they land on when the pod falls back to earth. If you are assisting you're orbital factory you should ensure that they are assisting from the side that the pods do not fall to back on least you lose your precious fabrication units.
If I recall correctly they've been doing that for a few builds at least already it's just part of the simulated nature of the game. I think if you set a rally point for the Orbital Factory you can keep the pieces from falling right on/next to the factory thought. Mike