Examples would be every interior in vanilla Skyrim. You haven't set lighting in your cell, I'm sure it was covered by the YT tutorials if not, the CK tutorials.
As for the npcs, incompatibilities, immersion breaking, quest breaking and I'm sure some other problems will arise. If the door doesn't fit, make it grow, shrink, or simply use another door. It's disorganised, like having your couch in the middle of the living room, your coffee table behind it, the TV to the side, vase in the doorway. It's more of a design thing. The whole smithing set up was the first thing I noticed and still recall.
I think I know why the grey face bug still exists. Try changing the names of your npcs to something not in the game before you press ctrl+f4.