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
Still an issue, as of 1.16.4, on MacOS version.
Validated the inconsistency with a USB mouse (works as intended when bound to scroll wheel) and when re-mapped to other keys or even the Macbook Pro trackpad (can'd drag to duplicate).