I have had the same issues with Sims 2 legacy. (1) A toddler disappeared after I closed the game for the night. She stills shows up in the family tree and their memories, but she is gone. (2) Parent sim visits a lot to buy clothes, and when he returns, the dog has vanished. When parent sim later goes back to buy more clothes, he comes back and oldest daughter is gone, too (and unlike with the toddler in the other family, she no longer shows up in the family tree and has the $subject name instead of her actual name when looking at the parents' memories). I tried recreating her with Tombstone of L & D, but when I quit the game with her as a teen, she disappeared again and I cannot reload the household at all, it crashes every time. (3) I went through university with several sims. Two of them were sisters. Upon graduating and returning to town, one of the sisters' image in the family bin looked corrupted, so I wasn't sure she would. Sure enough, I put her in with her fiance, and instead of being her, it was now a guy with a completely different name, though still engaged to the fiance. Replacement sim does not see the sister as related, but the sister does see him as her brother. However, when I left the lot to see what the sister thought, the replacement sim is no longer present. He shows up in the neighborhood view as being in the family and in relationships as still existing, but he's nowhere to be found.
I do not play with any mods and do not use cloud.
This game is currently unplayable. I can't spend hours working on sims, putting them through college or aging them up from babies, only for them to disappear at random. I'm very frustrated that this huge bug exists and hasn't been fixed yet. I never had issues like this when playing Sims 2 20ish years ago, so it's baffling that new (and significant) issues have been added when the game already existed for years. I'm really hoping EA fixes this soon so the game is playable again.