https://pastebin.com/g6pe8XSr

The error isn't very consistent as it seems to randomly show up doing various tasks involving luckperms. I deleted all of the groups, restarted the server and it still showed' up. The files are a migration from groupmanager.
LuckPerms.zip

here's an example with the error with default groups but with user data https://pastebin.com/KPK06q3P
The error doesn't show up when it's manually editing the file but only when the file is auto detected randomly to say there's been a modification to it even though nothing has changed.
LuckPerms.zip

Did you happen to edit permissions from the YAML files directly?

nope

Did you symlink the permission files/folder(s) so that you can sync permissions across the servers?

Set watch-files to false in the LP config.