Definitely caused by neighborhood stories allowing NPC's to move in and out and change jobs. Some NPC's obviously need to be flagged as other than normal NPC's. (like how some have the hidden "Weirdo" trait so that they cannot die.) The original Agnes and Agatha that cannot be found in household management move into the world or change jobs because there's nothing preventing that from happening. The game then tries to create new ones but creates them within the household management as "not in current world" residents. . They'll show up to work in the stall when created but then almost immediately leave.. So the game just creates clones of them over and over. I'm guessing, because it needs a sim with the hidden "crumplebottom" trait to work those stalls?
The same thing can happen with Father Winter in that he'll not actually be Father Winter if he moves into a residence or gets another job and so you can't ask him for presents when he shows up. However, since he does start as a manageable household this can be fixed by making sure he's "currently not in the world" and then turning off all the neighborhood story settings for him.
Basically neighborhood stories needs to be fixed so that it does not include certain NPC's.