If a domain has exceeded the allocated quota, but the check on its main directories do not reflect the correct space occupied, most probably is a problem of other directories which are located somewhere else but do have the same user as owner.

At least it happened withus where we had to do a quick backup from one production server to another (a temporary solution). While doing the backups, the new files copied had the same user-id as existing local users. By the end of the day, a few domains have exceeded their configured space limitations.

Whatever the situation, you should be able to find all the files which belong to a specific user in the filesystem. First the user-id of the linux user has to be found:
A quick check on /etc/passwd with the domainuser (if example.com, most probably your user is example)

cat /etc/passwd | grep $domainuser

$domainuser:x:765:750::/home/$domainuser:/usr/local/cpanel/bin/noshell

The first number is the userid, in this case 765

Now you can check the whole filesystem for resources allocated to this user:

find / -uid 765

If you find some user in some other directory, just fix the ownership information and you are good to go

Posted by xpo6

Software developer in the realm of AI, NLP and black magic.