How the west was lost:
I found a minor oversight in the mission where you need to escort cargo ships to a civilian station that is unhappy that you are seizing goods. There is a GNN shuttle broadcasting, if you shoot them with a lethal weapon they will run away but not panic. But if you shoot them with the Shield Breaker weapon nothing will happen and after a volley I got my fighter controls locked and I was court marshalled for shooting at friendlies.
EDIT: Same issue with Flail
EDIT: Also at the end of the mission I received the vocal command to return to base and saw it in the mission objectives and then I got the desertion message at the debrief about being confined to brig for abandoning the mission. However it is counting as a mission success.
EDIT: In the top paragraph of the debrief its complaining about my piloting skills as it says I lost some cargo ships. However I don't think any were lost but Ive been getting this message after a couple tries. I also noticed that the mission debrief doesnt take into account how I handled the dock workers, Neither shooting them or being passive was mentioned at the end, although I noticed killing the dock workers would cause additional enemies to spawn and dialogue to change in mission.