Pretty minor, but some of the tal shiar NPCs become untargetable at points. Only seen this a couple of times, though and is not mission breaking.
Gasko Blues Mission:
Commander Adar appears as an enemy as you meet him in the office, giving you a distinct clue as to what is about to occur. I havent tried it but you could probably kill him before the surprise and may prevent progression of the mission.
Neutral no more:
If you claim your ship before picking up the mission, it can't be completed Suggest you restrict access to the store until picking up the mission for the launch of LoR?
(Slight aside) Photonic tactical officer:
Get's injuries when killed, but is a superior photonic lifeform and isn't supposed to.