Ah! I am having this problem as well!
Sims who died before the Nov 15 update/Pets expansion are showing properly deceased in the family tree and I can still mourn them at their tombstones. (One odd thing though is that I had released all of their spirits before the update, but now they are all showing up as ghosts in-game as if I never released their spirits. The option to release their spirit is also not available, because I already had released their spirits once upon a time...)
Sims who have died since the update and have had their spirits released show as alive in the family tree and I cannot mourn them at their graves. They also have lost all ties to relationships via a "?" relative. So for instance, I had a pair of siblings in my town I created without a parent, so the parent shows as "?" icon on the family tree. Before the update, these types of sims and their families are still linked together in the family tree after dying. Since the update however, these types of sims have had their relationships void and their extended family removed from the family tree if I released their spirit to the netherworld (and only if they died/had spirit released SINCE the update. The trees are still intact for the families of "?" related sims who died before the update)
This is very frustrating and I hope there's a way to rectify this... I can't believe my family trees have been wrecked by this!
I should also note that I do not use any mods, and I have not noticed whether or not these sims are showing up in my unplayed household bin--I never even thought to look until I read that other people in this thread's "deceased" sims were. I'll have to look tomorrow, but it seems likely that they'll be there.
