Rectangle/Squares of Darkness randomly in the world

Please provide a screenshot with the debug screen enabled (hit the F3 key) demonstrating the issue.

Here's the screenshots with F3 debug.
Screen when outside of dark area

Screen when inside of dark area

a) Was the world even opened in 1.15x after having been open in 1.16.x?
b) If the world was updated from 1.15.x, did you using any server modifications while using that version?

 a) The world was generated in 1.15 but has been converted to 1.16 since the update been out and hasn't been opened in 1.15 since.
b) I was using PaperMC for 1.15, but since have been using 1.16 vanilla.

I want to say that this has been happening a lot recently. These didn't exist when the world was first converted, its been doing it for the last couple days. The only conclusion I can come to is corruption since some of the chunks were also swapped (which I used the mcaselector 1.13.1 to fix). The chunks have been fixed, but not these lighting bugs.

Alright, I'm a bit torn, since the world was opened in a heavily modified version of the game. Please try starting the server with these flags:
--forceUpgrade --eraseCache
That should hopefully get rid of the spots, but please be warned that it may take a while if the world is large.

So I'm back with an update. It seems to not have fixed it. It's did do something though. The shadows in some spots do disappear, but more appear in different areas. I'm most likely gonna contact paper to see if they have anything since I've heard of them having multiple lighting problems in the past. I don't really know why it carries over to my vanilla server though, especially since none of this happened until the last couple days, which is far from me last using paper and 1.15 

Maybe also check if using Paper for 1.16 makes the lighting issues disappear. So far, since the release of 1.16, we have not received any reports similar to this, so it might not just be Paper itself, but the specific plugins you were using in 1.15 that modifies the world in a specific way.

Please maybe also check if it happens on a brand new world.,

I've just done the command again and it now seemed to fix it. I haven't noticed any spots. I did try the latest version of Paper as well and have noticed that they came back. I really have no clue, but I'll report this to Paper. Sorry for the bothersome over these dumb issues. Was just getting very agitated by the swapping chunks and than having these lighting bugs come out of nowhere. I've also checked a new world and it doesn't seem to be affect on vanilla but it seems to be bugged on paper. Definitely a paper issue.

I've talked to some people from PaperMC and it's a issue on their end. Once again, so sorry for an issue that's not on the Vanilla end.

Thank you very much for clarifying, good luck to you and I hope they can solve it.