Our Scan Datastore task, and the Unknown Files monitor, will identify ANY file which is 'not known to vCenter'.
So, VMDK files could be included in the output- if they are orphaned
VMDK files. For example, virtual machines were removed from the vCenter inventory, but not deleted from the Datastore. Then those VMDK would be orphaned - and wasting space on your datastore. Exactly what the monitor and task were designed to find
Are those VMDK files attached to live, running VMs in the vCenter inventory?