This is a real issue but seems very sporadic. Only had a three or four spots in 20+ worlds that had issues like this.

One was in a mountain castle I had built. Just after the terrain / instance optimize pass update I started to see it. The area I had removed popped up through what I had built.

Then many worlds later there was a tower in the mountains I made into a rest house. I was going to cut away the dirt around the stairs to make it secure but every time I returned the area would fill back up partly and cover the stairs again. This I kind of figured was related to adding in the RNG stone tower on the side of the mountain making it a bit wonky... No big deal or anything just odd.

Most recently in my last world I had a spot in the Black Forest by a troll cave set into a steep river bank. I cut away and leveled an area to the rear of the troll cave entrance about the height of the top of the troll cave. Set up a forge in the area with smelters etc. but randomly I would return and find the ground dropped away or humped up. One hit with the level or pickax popped back to "normal" or what I had made correctly. After about twenty times it seems kind of stable? Seem to fix it less and less but have also move mostly away from the base and notice it only when using portals there.

Now that I think about it the area may be a bit unstable due to the troll cave model being put in there.

Do you have any RNG game structures in the area?