The problem happens when the disk quota file get corrupted on server. You can run the following command while logged into the server as root.
/scripts/fixquotas
If the above doest solve the issue try to run the following.
/scripts/fixquotas --force
It may give errors like the following, if the problem is not solved completely.
---
Resetting quota for abcde to 500 M
edquota: Quota write failed (id 32230): Invalid argument
Resetting quota for xyz to 500 M
edquota: Quota write failed (id 32010): Invalid argument
---
In that case, a quick reboot of the server will help to solve the problem. You may restart server via Power Panel.