I played a bit further, and found more bugs.
1: In "Tenderizer" Beta wing tries to jump out after the Galatea jumps, but never makes it before the next mission starts. Shouldn't they stick around? I know this happened in retail, but it always seemed strange to me.
2: In "Evangelist" the rest of Alpha jumps out after the Eva goes down. I think they should stay; after all, *you* don't get to leave. Again, this happened in retail too.
3: In "Doomsday", presumably Beta wing was supposed to transfer over from "Evangelist". However, a new Beta jumps in 5 seconds into the mission.
4: Also in "Doomsday" the Lucifer just appears out of nowhere. Doesn't jump in, apparently the Shivans have teleportation technology.
5: The Aquilae installation in "A Failure to Communicate" is frequently destroyed before it can tell everyone it's not going to make it.
6: In that same mission, Escape 2 and 3 appear *after* the installation has been reduced to rubble.
7: Also in the same mission, Epsilon wing's arrival is announced by a Terran pilot, despite being Vasudan fighters.
8: In "Clash of the Titans", you get to assign Gamma wing's loadout, despite Gamma not actually appearing in the mission. Present in retail.
9: Somewhere in between "Reaching the Zenith" and "Running the Gauntlet", I somehow acquired an SB Shaitan.
Take a look. I was flying a Medusa in "Reaching the Zenith", and the craft I flew in "Reaching the Gauntlet" acted like a Medusa in every respect but two: primary cannon placement and exterior model.