Ideas
I just noticed this is happening in my game as well. One of my Sims is duplicated twice in the family tree and looks like a ghost, and the ghost icon shows up when messages from her appear in the notifications (I thought she'd died off screen! But she's alive, the ghosts seem to be from the Skillful Sleep).
When I tried to switch back to her household to see what was going on, the game crashed (no mods/CC). So I went back in, loaded a different lot, and went to manage the families from that point and split her from her household and put her on a lot by herself, moved the rest of her family (the husband and two kids) to a new lot and bulldozed their old lot.
Then I went to her new lot and deleted the Skillful Sleep trait from her. Her ghost icons still appear in the family tree, but so far both her new single-Sim household and the new moved household with the husband/kids are functioning fine, but I'm nervous about trying to put the households back together. 😬
The Last Exception file that crash threw had this near the top: "temporary_clone_situation.py:107" which sounds like Skillful Sleep is the issue.