I'm noticing a lot of cases now where a ship or a whole wing of hostiles will just sit there and wait to die.
For instance, I went into FRED and set up two capital ships to come in, wait a few seconds, go beam free, and waste eachother. Only the friendly terran team ship shoots. I can open the mission back up, go to edit ships, change the friendly ship to hostile and the old hostile vasudan ship to friendly, and then only the vasudan shoots. If I check the box for all teams at war, then they both shoot, but the friendly shoots at me too.
This kept occuring in the sync campaign missions I played through yesterday as well. I'm now on CVS 2/25/2006 build.