Sounds like height map overflow.
Can be very annoying when this happens to a nearly finished map at a location where you can't just cover it with some trees...
Is the location where you have this bug very heigh? Most times I've experienced this bug, it was at high areas on my map.
In the past I could avoid or even "cure" this bug by using the 4gb patched exe from MudrunnerMod- but I don't know if this works with the new versions of MRMod.
Second solution is, to lower/ flatten the terrain until the bug is gone.