I know about the bug when a character wakes and decides to do whatever they want instead of what the player directs.
I am having difficulty with crew too, and I think it's the same fundamental problem, that when taking control of a crewmember you don't actually take control.
I think whatever is going on in the code needs looking at, basically when a player takes control of any char, they should have control unless the player clicks the auto-task option. I have had such a poor experience trying to manage a crewmember recently that I think this is an essential bug to fix now.