NO, you shouldn’t edit the rewirte.php file, it is part of the wp core file which not meant to be edited. WP already provided bunch of hooks that for you to customize/edit. The point is how you going to use them.
I not sure if this plugin is the real cause of it since others doesn’t have this problem (and this plugin did not use add_rewrite_tag() function). That’s why I ask you to change the theme to see if it is the theme compatibility issue. OR, there might be plugin compatible issue, which caused by conflicts with other plugin. In this case you will need to deactivate all of the plugins and reactivated them one by one to see which plugins is causing the problem.
From the error message, I don’t think the problem is caused by this plugin since this plugin doesn’t use add_rewrite_tag() function. You have to narrow it down to see which plugin/theme that calling for this function. This is the proper way to solve this issue.
Also show me the filter you said you want to add.