We have found that when Virtualmin creates backups for all websites in every one of them it creates .backup directory and leave it there until the whole backup(on all websites) finishes. This leads to clients receive emails for account over disk quota. This happens because after the current domains backup is finished the disk quota for the account is re-enabled. But because of left .backup folder for every domain in the account containing backup version of the domains files, databases etc. the account reach the quota and virtualmin send email to the client that the account is over quota.
I think that the backup script should delete .backup dir right after it finishes backup the current website and after the .backup is deleted to reset the quota back.