I've noticed those in the mantle of Sylva but just barely. They tend to be around stalagmites and stalactites. Maybe forms of unbreakable material, surface rocks as well, are disappearing but the game still recognizes them as there? That could explain why they (and I) are getting stuck. This was somewhat happening before update 1.13.121 but not to this extent. I'm running the Steam version maxed out so I think this is a mulit-platform issue. Though our situations may be slightly different.
I am running into the same issue. Mine has happened 3 times on the surface of Calidor and in the caves as well. My character is stuck on the surface as well. I tried to reset the game and now my save is unplayable. I have an image but I am unable to upload it.