This bug is related to Bug #211, but with group/domain quotas instead of user/mailbox quotas.
Apparently, Virtualmin seems to use the du command (or another similar method) to calculate domain quota usage. However, the operating system enforces these quotas based on the quota command, which can differ significantly. Virtualmin should use the quota command also to ensure there is no discrepancy between the disk usage and the quota enforcement.
Case in point: One of the domains we host has its quota set to 1.20 GB. The Filesystem Quotas Webmin module shows their usage at 99%, or 1226/1229 MB. However, the Virtualmin module shows only 93% usage, or 1139 MB. This is a critical discrepancy, because the it appears that the domain still has some room for operation, when in fact it is almost at 100%. The result is that FTP transfers are failing, e-mail messages are bouncing, etc., even though these problems shouldn't be happening as reported by Virtualmin.