Does it pop into place eventually if you give it time before landing? I've had some of mine do this as well, but if I just cruise slow before landing, it will snap into proper position. If I land though, it seems to 'lock' into that position until I leave and come back again.

It happens to me on one of my "main" bases. Picture attached (NEXT-era "grass" but it happens now in Beyond, too). I'll give that a try. It happens when dropping in via teleporter as well, though.

In my case I was attributing the odd behavior to having found an old "wild" base location (without a base computer, though). The spot is a smooth, flat circle about 300 units in diameter and it generates a moment after the general terrain. The program-generated foliage, rocks, etc. are all correctly placed on the surface of the ground, it's only my own trees and other material which becomes sunken.

Moral: Always build an elevated base, at least one "wall height" above the ground.

It mostly happens when I return by teleporter.