I have been getting this issue for about 4 months now (the missing texture error, not sure about the other) , and it happens probably 40% of the time when I make an atlas. It usually just results in there not being a texture created, and the progress bar staying up, but can be fixed by generating it again.
As for a reproducible, I have had this error on a completely new project when I was trying to reproduce the reverting prefab issue. So simply importing ngui, importing two textures, then creating an atlas should be enough to reproduce it.
