VMware Cloud Director 10.4.x
The issue with the VMs in the stranded folder in vCenter it's usually related when VCD deletes a VM, but that VM is actually not deleted from VC/ESX.
The VM is then discovered again in VDC RP, but VCD does not know whom it belongs and puts it into stranded VM folder in VC.
In terms of multiple folders, VCD will only attempt to create the stranded items folder only if it cannot find it. The folder duplication can happen because the already existing stranded folder has a different name from the one VCD would use.
This could happen due to temporary issues synching with VC during the process or VC-ESXi connectivity issues.
The VM in vCenter stranded folder can be deleted after confirming they do not exist in VCD anymore.