Certain meshes have flickering black splotches which upon closer inspection say "Your scene contains a skydome mesh with a sky material but it does not cover that part of the screen"

[Daffrendo]

This may have to do with light baking and light mode. Try to isolate the phenomenon, setting a single light to see if it causes the blotches, then change that light between Stationary, Static, and Moveable. Maybe this could help.