WHMCS has disk space overage billing option. If customer uses more disk space than their subscription allows then WHMCS will charge overage. In case customer buys additional disk space (via WHMCS configurable options), WHMCS will look at additional disk purchased and will not charge overage.
However, in order for WHMCS to look at additional disk purchased, the configurable option must be named Disk Space. If it's not named Disk Space then WHMCS will not know that additional disk has been purchased. This is documented at http://docs.whmcs.com/Disk_Space_and_Bandwidth_Overage_Billing
Plesk Automation (PA) WHMCS module uses configurable options with names like Additional disk space however WHMCS must use Disk Space. Since the names are different WHMCS does not know if customer purchased additional disk space which results in overage charges that they should not be getting.
The behavior was considered as internal software issue with PPA-2335. It was fixed in PA 11.5 MU#11.
In order to fix the issue please follow 'Installation Instructions' from the article.