I experienced similar issue with a tenant having few vApps showing double storage consumption than VMs inside the vApp.
This is a known issue resolved on vCD 9.5 onwards. By opening a case with support they can confirm that and advise you to upgrade
I recommend you upgrade VCD
Moving VMs to new vApps and doing any other work on will not resolve the issue unfortunately
As workaround you can increase the storage quota to allow tenant consume that capacity until you find a way to upgrade or migrate
If you have concern about consumption having a dedicated Datastore for those VMs can make the trick of limiting those machines.
Thank you for taking time in answering my question.
Unfortunately, I have a slightly different problem. vCD itself and vApps report proper usage of storage space, I've even went to VCD DB and checked that value. It only miscalculates usage when trying to change resources. Even checked vSphere and there were no errors as well.
My only option, that helped, was to add another VDC and have tenant to migrate to a new VDC.