Just noticed the other day while playing with a friend against AI that even though we were on the same team but using different armies (not shared armies) that whenever I tried to go assist his units or use my fabs to help him build something to assist his fabs, it would attack and demolish his buildings or kill his units.... so I'm wondering if that is supposed to happen? because thats not very team'd like heh... or if its just a bug and not supposed to attack your team mates?
As long as I understand alliance features under heavily development, so it's not just "bug", but incomplete feature. There was task on bugtracker about issue that when area attack used your units will attack your ally. You can't damage ally units with attack actually, but you still able to reclaim them. I suppose this behavior with builders appear because they don't actually have "attack " action, but "reclaim". So their default behavior for alliance units is reclaim. Still if you actually choose "assist" or "repair" from menu or hotkey this should work properly because you still able to repair/assist enemy stuff.