How to Fix Cpanel/WHM quota issues.
Cpanel/WHM sometimes has problems with the user quota files causing all users accounts to have unlimited disk space available or 0 megs of disk space in use.
Login to SSH using as root user. Then run the following command
Try to find other files owned by the user.
find -user USER_HERE | more
This will list all files owned by this user that could be affecting the quota reported by Cpanel.
To find all directory, run
find -user USER_HERE -type d
To find all files, run
find -user USER_HERE -type f