How to Fix cPanel/WHM Quotas?
2) Run the following command as root user.
1) Find the user account where the quotas are incorrect and login to your server in SSH as root.
2) Go to the users folder and check their disk space being used.
5) check /etc/passwd and /etc/shadow to make sure there is no weirdness where the username shows up multiple times.
4) Try finding other files owned by the user.
find -user username | more
5) Uncompressed backups can cause quota problems, ensure your backups are compressed in the WHM backup options.
6) After your determine the source of the files and remove them then run