That sounds pretty bad, as you will need both players shooting them pesky aliens if you're going for the ach. I played through Hydroponics in local co-op, and me and my friend found it pretty easy tbh. However, the first co-op mission was way harder I thought, so all I can say is maybe try playing Hydroponics?
As for the glitch, I cannot speculate as I haven't played co-op on Xbox Live, so perhaps its an online glitch? You could try waiting for the patch Team 17 have promised, or you could even go to their forums and post a new thread, explaining the glitch to them. They seem pretty helpful over there.
Hope it gets sorted for you soon!