Custom Taxonomy breaking pages permalinks

Can you provide a link to your site and a little more explanation on what you are trying to achieve?

Here’s a shot in the dark guess.

Archives shows content of type ‘post’, but you can alter it to include custom post types. Add this filter to your functions.php file:

function namespace_add_custom_types( $query ) {
 if( is_category() || is_tag() && empty( $query->query_vars['suppress_filters'] ) ) {
  $query->set( 'post_type', array(
   'post', 'nav_menu_item', 'your-custom-post-type-here'
      ));
    return $query;
  }
}
add_filter( 'pre_get_posts', 'namespace_add_custom_types' );