Really, this is unusual? I dunno, the TS3 game I'm playing has a reputation for having things like family trees fall apart every time the player sneezes hard (and in this neck of the woods it is actually allergy season for many of us). So what game is everyone else here playing? :)
But seriously, I think this kind of thing is to be expected, and that's partly why the MC commands exist and are as easy to use as they are. Glad that's being helpful.
I never experienced family trees falling apart first-hand myself though, maybe one time with a sim who was actually supposed to only be a step to one parent because they were a Science Center clone of the other. Certainly I got the age randomization from throwing sims into CAS that everyone "loves" so much. But to be fair in my earlier non-mod (or non-NRaas) days, most of the sims I played were single or recently partnered with no or not very many kids yet.