I'm still learning the ropes of the game. My last game was a FFA wherein I played as the Advent for the first time against two TECs.
Although I received numerous missions from both computer players that generally involved sabotaging the Other Guy, the computer players made no attempts to directly attack each other. In fact unlike myself, they were able to leave in single, defenseless colony ships in another computer's system without being attacked. Not once did they fire upon each other; only me. There was no where on the Diplomacy screen could I find a "Relations" chart that showed that they were actually allied against me, but when a giant fleet of one AI followed by a Me-Too fleet of the other attacked me, I knew I was playing a 1vs2 game (And promptly quit.)
And no, I didn't setup the game with locked teams with two A.I.s both on Team 2, they were clearly separated. So what gives? Why wouldn't the A.I.s attack each other? It won't always be like this, will it?
Another thing, I've found all of my attempts to curry favor with either opposing faction was inevitably thwarted as they would sent a scout ship into my system to be instantly obliterated along with any positive relation gains I'd made. Although I COULD turn off Auto-Attack, that would mean I wouldn't have that instantly obliteration against the OTHER opponent(s). Is there any way to set up a "Do not attack Player X" outside of having a cease fire/peace/alliance agreement?