Just making sure. Under which tab in Manage Households are the ones that have been having the babies? My Households or Other Households? Sims that you have played but are now under the "Other Households" tab will be subject to the Neighborhood stories actions. If you've moved a household to Other, they will be seen by the game as unplayed. You can tell by the color of the plumbbob icon.
Hope this helps.
This is possibly a dumb question, but... are you using any mods with Risky Woohoo? I did get a surprise baby in one of my played households after rotating away, but I also have risky woohoo on, so I blamed risky woohoo and assumed I just forgot to check and see if she was pregnant before leaving.
