Highways which are not part of a relation
the scrpit not include the ways belong relations
Thanks for reminding me it, I've added the documentation. https://wiki.openstreetmap.org/wiki/JOSM/Plugins/To-fix and on the list of plug-in https://wiki.openstreetmap.org/wiki/Template:JOSMPlugins
might be it happen because your JOSM is old version, the plugin supports from version 8151 https://github.com/osmlab/tofix-plugin/blob/master/build.xml#L5,
Let me know if it is not working.