Crew Stop Working Stats Bug
Had two marine crewmembers get injured during a boarding operation, so I got the "Crew Penalty" debuff since that dropped my stats below the usability threshold for some of my equipment. No problem, went to an allied world, and repaired/healed all. Undocked, only to notice I still had the debuff (I didn't change my loadout at all). Went back to check my crew and noticed that the marines had fallen below 50 Happiness, so I figured they had stopped working (which I understand is an intended game mechanic). So I paid them both up to 100 loyalty, but the "Crew Penalty" debuff remained. When I removed one of the marines my stats dropped by his skills, but they were lower than they should have been. So as an experiment, I added a completely different crewmember to take his place (just an extra guy I had in my cargo hold) then my stats went up by the new guys stats PLUS the old guys stats.
I think the bug might have to do with losing crewmember stats due to both injury and low happiness at the same time, or something on that order.