1) The whole "lure the Shivans to the Renenet" thing is broken. The directive uses one technique, and the goal uses another. And those techniques are not 100% reliable; it's very easy for the mission to dead-end because of a hole in the logic, even though you did everything you were supposed to.
2) As a corollary to (1), the rest of Alpha wing should break formation if they get attacked. Currently they're slaved to following waypoints, which means that 9 times out of 10, the Shivans wipe them out before they can be lured in range of the Renenet.
3) The Renenet says "Command, we have sanitized the area" when you destroy the first two wings of fighters, but the third wing has already arrived. The third wing should probably be cued to arrive only after the freighter has arrived.
4) The Renenet often says "Alpha, your vessel must be no less than 3,000 meters from the center of the portal" even though I am, in fact, more than 3,000 meters away.
5) The "Protect Renrnrt" goal (which should be spell-checked) becomes true immediately upon the Sathanas jumping in. It should only become true after the Renenet departs.
6) Use "$Debriefing Success Music: Average" (an undocumented feature!) at the end of the music section so that the Average music plays instead of the Success music. (On that note, do the same for Their Finest Hour.)
Those are the ones I could think of off the top of my head. There may be more.