In cPanel, on the homepage in the left-hand column, you will see a "Disk Space Usage" statistic. You will also notice an icon in cPanel called "disk usage viewer"
Sometimes, (usually) these two items will not be the same number.
There are 2 reasons that we know of for this problem currently, however, the disk usage calculation on the cPanel main page is the correct figure in all cases.
The most common for the "disk usage viewer" inaccuracies is that your cPanel is caching old quota information and you recently deleted unneeded files. The way to clear this cache is to use the option in the disk usage viewer called (as of this writing)
The other option is to navigate to the top level of your site "/" and delete the file called .cpanel_ducache which you can see using the file manager inside of your control panel.
The second most common problem is due to sites that have an excessive number of files installed on them. The disk usage view does not account for file system overhead like the cPanel main page does, and because of that, tiny bits of overhead data can really start to add up.
Directly quoted from cPanel support:
What does this mean to you? it means basically the current disk usage view should be considered a "ballpark" estimate and is a good place to look for general ideas of where disk usage is being most consumed, and that the ACTUAL total disk usage being consumed by your account is listed on the cPanel main page.