Yes a lot of people have had this problem. Including duplicated settings files too. I personally wouldn’t use iCloud or OneDrive for my notes ever. For some people it works fine, but wow I don’t trust it.
And @sagerwly Ryan already said, but I’ll say it more directly: Don’t mix multiple syncing tools!
And everyone: Don’t consider syncing tools as a backup. Make sure to keep backups in some other way too.
What “cloud solution” are you talking about? Are you also mixing a 2nd sync app on top of iCloud?