So I was running "Collateral Damage" just a little bit ago, and I noticed something quite strange.
The mission started normally and remained normal single player until I beamed back up to my ship. To my surprise, I was suddenly team leader of a team that I never started. We finished the mission pretty easily, but the darn thing bugged on me so we had to start over.
No problem, we both go back into the Hotep system. The mission is now scaled to two people, but we went through it with little trouble. Beam back up to the ship and suddenly... there's another ship in my team that I didn't start.
The mission completed the second time, but I'm still a little puzzled as to what happened.