This probably isn't the place but I recently replayed both FS1 and FS2.
In more than a few FS2 missions, the wingmen weren't obeying any "engage enemy/form on my wing" orders, and just sat there like idiot puppets. They would react when I would order them to destroy my target, but then after that they'd just disengage and float while the enemy killed them.
Also, in the final mission, support was bugged and wasn't arriving (deploying support ship now, please stand by x infinity), and to top it all off, when I jumped out in the node as the supernova was counting down, I got a debriefing instead of a cutscene, with "no debriefing for mission blahblahblah".
There were also horrific errors with where the AI was jumping in, for example in the final mission, the final wings of Seraphim bombers would jump directly on top of the final Argo transports, launching their ordinance as they came out of subspace (no chance to intercept their bombs), and then just sit there without moving, colliding with eachother.
Weird **** abounds throughout the whole campaign, those are just some of the things I remember off the top of my head.
Also, is the Sathanas vs. Colossus mission ever going to be fixed so that those two are positioned correctly and the Colossus doesn't spasm like a baseball bat?