IF it helps the NPCs seem to be warping to areas inaccessible by PCs. For example in the Stranded mission in the area by the engineering deck there are 2 doors. 1 on the left facing the engines and 1 on the right. There's nothing behind door number 2 but that appears where all of the NPCs are warping to when they bug.
For this mission there is a small workaround. Die so you spawn in the engineering section and one of your security team will promptly go in and kill the NPC there allowing completion of the mission. You must have your crew set to attack your target and then you can usually get a target (but not fire on) the Orion that bugs into there. So maybe there's NPCs spawning out of the map causing the rest of them (BOFFs and enemies alike) to bug out?
This seems fairly similar to the issues that were happening in the exploration missions when NPCs would go under ground and the BOFFs would promptly do their job and go after them.
My experience has been that they always warp to a spot that the PC can't get to at the end of the map regardless of the mission.