I would assume the difficulty comes from there being three "teams" right now: Aliens, Civvies, and You. The Aliens are keyed to attack all other teams. I would assume that this code carries over to the Civvies, though they are unarmed by default. There is probably some element preventing them from using alien weapons dropped on the field, maybe because their 'team' hasn't researched them yet, but if they can get human default weapons dropped by your side...
Now, an interesting experiment might be seeing if you could get a Civvy to pick up a Grenade Launcher dropped by a glitch-Ort, and whether the Civvy will then attack the nearest alien, or come blindly gunning for your guys...