What you have described can happen if you revert an ongoing game session to the Main Menu and startup or load a different save without having quit the game all the way to the Desktop (or Origin if relevant) in between. There is always a risk that the sim data from the prior game session doesn't get entirely released from RAM in between and then gets super-imposed on the next game/world loaded up with all kinds of mismatched results.
The NRaas Traveler mod is known to make this more of a risk, but it also happens to players without it and with no mods at all.