It is accompanied here by 8K grass texture which doesn't seem to have the same problem.
My guess would be that 256 px texture is assumed to have a uniform size (8K) with the rest of the atlas and as a result (non-existing) black face is selected for some faces. Just guessing, though.
Pawlost
commented
5 years ago
Black faces appear on custom 256 px texture.
It is accompanied here by 8K grass texture which doesn't seem to have the same problem.
My guess would be that 256 px texture is assumed to have a uniform size (8K) with the rest of the atlas and as a result (non-existing) black face is selected for some faces. Just guessing, though.