This might be an exploit BUT it's a reverse exploit that the NPCs are currently using to attack you when you can't attack them. Set your BOFFs/Ground crew to attack your target. I found an Orion in the Stranded mission was hiding where I couldn't get him BUT was able to get a target. Set my crew to attack target and I was able to complete the mission. Betting this will work for a lot of other bugged missions as well. Your crew will WARP to where the NPC is and kill it. Basically it's having your crew take out the NPCs that hide in places you cant' get to. Heck the Orion in the Stranded mission was hiding behind a wall in the engineering area where there was no room behind it but shooting through the wall.
Until they fix the missions this might at least allow for completion of missions.