Is this still a problem? Cloning a debian VM works for me on FreeNAS-11.1-U6. What OS is running in your VM? Have you checked that NIC, VNC and disk devices are still correctly attached to the VM?
Could you (re)post any screen caps so they are legible. Before you re-test check you don't have any bhyve processes running on VMs that where not stopped properly after failed boots. A combination of bhyvectl --force-poweroff --vm=xxxx
and bhvyectl --destroy --vm=xxxx
, or the destroy command on its own, should clear those.
Also at the FreeNAS CLI have a look at the middlewared.log to see what clues it provides as you boot the original and clone VM with tail -f /var/log/middlewared.log