How to remove an orphaned object from permissions

Source: communities.vmware.com

Get-VIPermission -Principal "User/Group name" | FL

Output:

EntityId      : Datacenter-datacenter-XXXX
Entity        : User/Group name
Role          : Role Name
Principal     : User/Group name
Propagate     : True
IsGroup       : True

There you can see the EntityID / Entity and Principal for the group also the orphand one will show up.

Get-VIPermission -Entity "vm1.briemle.lab" -Principal "briemle.lab\VMware-User" | Remove-VIPermission
Perform operation?
Removing permission on entity 'vm1.briemle.lab' for principal 'briemle.lab\VMware-User' and role 'Administrator'
[Y] Yes  [A] Yes to All  [N] No  [L] No to All  [S] Suspend  [?] Help (default is "Y"):

So you can verify the EntityId and delete your orphaned one and ignore the rest.