I have no idea as to why this happens, but I can confirm that when exiting to the overworld via Nether Portal I experience severe lighting glitches all around. I think it correlates to when entering the nether at night time and exiting to the over world in the day time. To fix some of these, I am able to place a block and update the chunk which does the trick. But others stick in place and don't change after placing and or removing a block, the only option and fix after that is to save and quit, then reload my world.