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. Please find the below steps in fixing any quota issues with Cpanel manually or automated.

When you face Quotas Issues, first try the below steps.
1) Log into your server through SSH as the root user.
2) Run the following command /scripts/fixquotas.

If it is not fixed then try below steps.
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.
$ cd /home/username
$ du -h or try du -hs
3) 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) This will list all files owned by this user that could be affecting the quota reported by Cpanel.
6) Uncompressed backups can cause quota problems, ensure your backups are compressed in the WHM backup options.
7) After your determine the source of the files, remove them and then run the below command.
$ /scripts/fixquotas
8) If the issue still exists then we need to debug more.