While playing with standard NotEye settings and exploring dungeons, the graphical system gets confused and overlays the ASCII graphics over top of the NotEye graphics.
This can be resolved by saving the game, and quitting from ADOM completely, however upon re-encountering the reason for the overlap the issue arises again.
In the game (I will link to Thomas) it appears to occur when encountering water tiles on D6 of the CoC, while being on the level with the water is fine, once the water comes into sight the issue arises.