This one is a major spoiler for late game so the details will be in spoiler tags here.
Spoiler:
After the funeral for Sarah (or the alternative companion if you saved her on The Eye) [Missed Beyond Measure], leaving The Lodge resulted in the game assigning the now dead NPC as my current companion AND making her available for my crew. This clearly should NOT be happening at this stage of things since she's dead.
Further, it made it impossible to remove her from the slot until well after all of the current crew members boarded my ship or otherwise returned to their normal schedules. Even after that point though, I ended up having to return to The Lodge and take Vasco on as my new companion since he was the only one the game would let me take.
The whole while, if you look at your crew assignments, she's listed as unassigned and on The Eye. Obviously she is not there if you go to find her.
I have no idea how something like this gets past QA, but here we are.
It's been reported to Bethesda.