We've got a shader rewrite planned in coming updates, that will hopefully address a lot of these visual artifacts.
:Technical info, if you're curious.
We're dealing with really large distances in the game, and there's not enough resolution available in a convential depth buffer to handle it. This causes rendering issues by incorrect rounding of faces. So you'll get triangles drawn in the wrong order. In this case the triangles of the surface are rendering over the atmosphere.
Georg developed tech for a logarithmic Z-buffer, that should stop these sort of glitches from happening anymore. Unfortunately, we haven't been able finish implementing it, due to a Unity lighting engine bug. It was just fixed in a recent Unity patch, so we should be able to move forward with our planned upgrades.