If the base system uses proprietary video drivers (eg nvidia) and the target system uses open video drivers, then the target will boot, but have only a console and no working graphic terminal.

A possible workaround is to edit in exclude script
(/usr/lib/refractasnapshot/snapshot_exclude.list)

to add:
  /etc/X11/xorg.conf
  /etc/modules.d/blacklist

This still may not boot the target so
1) revert the base system to open video drivers
2) rebuild grub: # update-grub2
3) move /etc/X11/xorg.conf to /etc/X11/xorg.conf.bak

rerun refractasnapshot

thanks for a great tool!