Cloning blocks doesn't only create lag spikes (MC-123584), it also makes the (internal) server lag. I couldn't reproduce it with /fill so far.
How to reproduce:
Execute a /clone command every tick, using a repeating command block or function.
Conditions:
It seems like this issue only occurs when two or more /clone commands are activated in a short amount of time. In addition to that the player has to be near the affected area and this issue does not occur when the player is in specator mode. The gamerule "spectatorsGenerateChunks" makes no difference.
Since it's cloning the same area, there shouldn't be any light updates causing this.
The attached video shows how many milliseconds Minecraft needs to process one game tick (using this methode: https://youtu.be/w_43hYVxYa0)
The lag is cause by one /clone command cloning ~13,000 blocks.
Please check if that's still an issue for you in the latest version of Minecraft.