This behaviour is caused by a known issue where the Cloud Director Tenant Portal UI does not make the Copy action available for Powered-On vApps.
This is a known issue affecting VMware Cloud Director 10.6.1.
To workaround the issue the individual vApp VMs can be cloned to a new vApp, Copy a Virtual Machine to a Different vApp in the VMware Cloud Director Tenant Portal.
Alternatively the Cloud Director API can be used to clone the Powered-On vApp, VMware Cloud Director API CloneVApp.