Possibly you are hitting the same issue mentioned on KB Cloned virtual machines that has an IPv6 address keeps both addresses (2040850) ? Please also review the vSphere IPv6 Connectivity section - https://docs.vmware.com/en/VMware-vSphere/6.0/com.vmware.vsphere.networking.doc/GUID-6BC115DF-4EC5-409E-8B74-45525E966F0F.html
The KB applys to vCenter 5.1. We are running a newer version of vCenter. I' ve found out that there is an attribute IPV6Spec from the object VcCustomizationIPSettings used at the workflow where the IPv6 configurations should be set. But after changing the workflow I'm getting Fault.NicSettingMismatch.Summary error.
It would be very good if someone of the vCO team could develop a Clone VM workflow with IPv6 to get as a start point.