virt-clone only takes care of the libvirt config but won't touch unique identifiers in your disk image.
/etc/machine-id isn't the only thing to worry about when duplicating a VM - think SSH host key, DHCP leases, various filesystem UUIDs, log files, MAC addresses in ifcfg-* files and udev-persistent-net rules...
You can use virt-sysprep[1] to clean up a disk image.