Quotas can be kind of a pain sometimes. If your accounts are showing 0 disk space used, be sure that you have enabled quotas in cPanel. Most people select this option during the initial cPanel configuration, but you can always enabled them later in WHM -> Initial Quota Setup. Once you’ve done that, let’s ensure that quotas are enabled on your partitions. You really only need them enabled on /home and /var. If you have a single partition, enable them on /.

If you needed to add usrquota to your /home partition, save your changes in /etc/fstab, and remount /home with
mount -o remount /home
Now we can run the following to repair the quotas:
/scripts/fixquotas
There are still plenty more ways that quotas can break, and dozens of errors associated with broken quotas, which I hope to go into deeper in the future.