I'm noticing this issue on my 1.16.4 server as well. More details:
The dark spots appear to be generated from faulty blocks in mid-air, mostly high up - from 25-50 blocks above sea level
Replacing all the blocks at that faulty Y-value of the chunk, then breaking those blocks, eliminates it for a time
Restarting the server makes them return
David Snow
I'm noticing this issue on my 1.16.4 server as well. More details:
The dark spots appear to be generated from faulty blocks in mid-air, mostly high up - from 25-50 blocks above sea level
Replacing all the blocks at that faulty Y-value of the chunk, then breaking those blocks, eliminates it for a time
Restarting the server makes them return