Bug in "Website Quota (Harddisk)"
If you list website's quota (Sites->Statisticas->Website Quota (Harddisk)), it will be listed exactly the double of the quota a site has assigned.
For example, for a site with a 2 GB harddisk quota, you will see 4096/4098 MB listed.
I have listed quotas on system (repquota -avug), and they are correctly assigned, so it must be a bug in ISPConfig