Sometimes, you may get the email quotas exceeded but your mailbox is actually not using so much spaces.
The mailbox email@example.com is full or very close to full.
You should remove some emails from the box as soon as possible to prevent
losing any future mail.
This mailbox is currently 100.00% (251.76/250.00 Megs) full.
There do have 2 methods to fix this issue.
1. You may go to the mail directories of your virtual account, look for the mailbox account and remove the maildirsize file.
2. If the above method not able to fix your problem, run the following command.
/scripts/generate_maildirsize –force username
Where the username is your cPanel username.