I have now turned it off. I'm not really fond of the game deleting my families at random because single males keep asexually popping out kids. I am perfectly capable of keeping the neighborhood populated & interesting without the story progression effing everything up. I turned it off and I'm keeping it off.
This happened to me also, I had a family of 2 sims in a custom house I made. I wound up splitting them up and moving them into separate houses. Come back later and the female is gone and the male is back in my custom house and has a child all of a sudden with no mother.