This happened in Riften.
Whenever there is a lightning storm, ALL of the npcs (including workers, children etc.) go into the inn to seek shelter, despite the fact that the mod configuration clearly says everyone EXCEPT workers will seek shelter during such an event. And adopted children (in my case Lucia) will remain in the inn and won't listen to any orders i give her such as "go home and do your chores".... it seems that children become stubborn due to thunderstorms because of this.
The only "fix" I found to this was to completely disable the "Seek shelter" option entirely. Is there a way that I can keep this option turned on without any issues? I like the fact that npcs seek shelter during a thunderstorm, however, not to the extent where a town is completely empty inside their houses, even the merchants.
P.S. I don't know whether this was due to a mod conflict, or just a bug in the mod itself, but any advice would be greatly appreciated.