I have ran into issues several times where air units travel through the surface of the planet. There is no visible elevation difference in the areas where this has occurred. Air units have also sometimes move inside buildings. When air fabrication units are inside the planet or building, they do not fabricate as expected and have to be moved before fabrication can start. Seems like its probably an issue where the actual elevation of the planet/building is higher than what the air units perceive the elevation to be, thus no elevation adjustment is done.