Ideas
I've previously paid almost zero attention to Family Trees, but what a quick look shows is that Family Tress that include Alien Abductions or maybe just Aliens in general (the Aliens I've played all started out as NPC.s) - I don't know - seem to have ended up with jumbled relationships.
Also, if the parents/grandparents started out as NPC's or pre-mades and have since died, they now show up as unknown with blank portraits. This seems to be true even if I played with the parents/grandparents as well as the children. Seems kind of sad.
Not all my Sims had parents who were Married. (I always fail at Wedding Events, so I just don't bother.) In some cases these Sims now have no parents, if their parents are dead. Especially if their parents were NPC's or pre-mades.
Haven't gone through all my households, yet.
I don't know if any of this will effect my gameplay when the Royalty & Legacy Expansion Pack comes out.