Looks like orphaned permission definitions are not shown anywhere. I think this is a bug. Not specifying a permission group when saving a definition results in an error; same should be done if an interface group is not specified.
Code:
Please enter a value for the required field 'permission_group_id'.
As a workaround, you can manually visit:
admin.php?permissions/permission/<<permission_group_id>>/<<permission_id>>/edit