If your cpanel is showing wrong mailbox quota than the actual usage 

You  need to Do the following steps to get it fixed.

Login to your server with root user and check the actual usage of email account

#cd  /home/username/mail/domain.rld /

#du -sch emailaccount

If you found the difference in actual usage and cpanel results then

#cd /home/username/mail/domain.com/emailaccount

# rm -f maildirsize

Now login to your cpanel >> email >> email account option > Reset Quota  and reset  the quota of the account.