Some things to do:
Step 1. Find the user account where the quotas are incorrect and SSH to your server as root.
Step 2. Go to the users folder and check their disk space being used.
cd /home/username
du -h or try du -hs
Step 3. Check /etc/passwd and /etc/shadow to make sure there is no weirdness where the username shows up multiple times.
Step 4. Try finding other files owned by the user.
find -user username | more
This will list all files owned by this user that could be affecting the quota
reported by cPanel.
Step 5. Uncompressed backups can cause quota problems, ensure your backups are
compressed in the WHM backup options.
Step 6. After your determine the source of the files and remove them ,then run /
scripts/fixquotas
