This phenomenon is occurring in a few meshes, while many others are perfectly fine.
Two are meshes with large dimensions, though they don't have a huge number of vertices - one has 12,000 and the other has 31,000
This object is not that large or complex. It had ngon circle end caps that I converted to triangles, the rest is neat quads. We have been exporting with the add-on that exports to .escn. (Actually, we modified that a bit to exports as .tscn and export groups as separate files, but it's not a change that should affect this.)
This mesh is 1 km across, but it only has 31,000 vertices. It has distortion like this around all the scenes that are embedded in it, like the one on the darker grey ground here. There are gaps and incursions all around their edges. The following images is a very similar case, it is a mesh 600 m across with 12,000 vertices. This one has even more openings in it for buildings, and all of those openings have misalignments all around the edges
The common characteristic here seems to be that these are meshes with holes in them. Perhaps this is a clue. We have no idea here as to what to do.
We have a repo here - https://github.com/briligg/Moonwards-Virtual-Moon. Everything has been broken up, with the meshes stored as binaries so they load faster, so I can't really point to the specific files. The zip download is 105 MB. If there is any way I can give more useful information without you downloading all that, please let me know. I hope you can give us some guidance.