I have this problem as well. I have a tavern with a large stables with various animals on a mountain top. Most of my tavern patrons and animals consistently fall through halfway in to the foundation they stand on every time I log on. The base is rather large, and I’m uncertain if that has anything to do with it. But at the same time, I’ve also built a huge pyramid where I don’t have the issue at all.
The area is just outside where Al-Merayah used to be on the mountain top.
I run on a dedicated server without any mods whatsoever, just the base game. I can share files/access to the server if needed for investigation.