Light from nowhere?

I got the same.

Save file attached

Perfect Spacepad.sav

I have had this same thing happen. I cannot figure out how to reproduce it. When you save and reload the game, it fixed it for me. 

I guess the most obvious reason would be the game not "redrawing" tiles where the light was left by any kind of light source

Also, another kindof:

Dupe keeps waking up even though there is no light around at all

Optimistic Timeline.sav

I just experienced the same thing. Even after killing off all shine bugs and closing the room off completely, my bedroom was still marked 'well lit'. Quitting to menu and re-loading the game fixed it.