Dont know if all of this has been brought up (I presume it has), but I'll add it anyway just in case.
Flying through Sector Space has a few minor details that really disturbs me. For example:
1. After leaving a mission I often bring up my inventory to check what new stuff I have. At the same time being near a planet often brings up the "enter mission" bar, and even if I'm not klicking on the actual bar the game still think I want to re-enter the mission when I*m actually klicking around in the inventory.
2. Same goes for the merchants. I often get a "I'm sorry, but I dont have time for you anymore".. WTF do I care, I wasnt talking to you in the first place! Stupid trader. I can get these messages when I travel to another star and pass one of the merchants, at the same time as I'm klicking around inventory or paperdoll etc..