I was having an issue in my main save with homeless Sims suddenly moving into empty residential lots, so I think Neighborhood Stories is bugged. Because of this, I decided to play around with the new EP in a new save so I don't compromise my years-long invested households. I would recommend experimenting with a new save to see if it's still happening.
Also, it could have something to do with MC Command. Some of their settings are by default, set on a Story Progression function similar to Sims 3 and would need to be changed to prevent it. I do not use the Population, Career or Pregnancy modules (for now) in my game because there's a lot of settings and I can't remember which ones to change to get it back to "normal". You could try doing this as well.
Also, a good thing to try is to temporarily remove your mods folder and set it aside, delete the localthumbcache file (I also delete the avatarcache) in your Sims 4 folder (the game will generate a new one on startup) and do a game repair in the EA app. When that's finished, put your mods folder back in and start up, see if anything changes.
I've come to habitually delete those cache files and do game repairs every so often, but I always remove my mods folder first, just in case.
Side note: MC Command just updated again as of Thursday - I got an email from Deaderpool's Patreon, so if you haven't grabbed the new one, you should do that too, it might help.