How to filter by custom post type in taxonomy archive pages

That is the normal behaviour. If you go the archive of one taxonomy term you will get all posts, of any type, with this taxonomy term.

One solution can be, for example, adding ?custom_type=files or ?custom_type=questions to your URLs and alter the main query in the pre_get_posts filter:

add_action( 'pre_get_posts', 'my_pre_get_post' );
function my_pre_get_post($query){
    if(!empty($_GET['custom_type'])){

       //limit the filter to frontend, main query and archive pages
       if($query->is_main_query() && !is_admin() && $query->is_archive ) {

          $query->set('post_type',sanitize_text_field($_GET['custom_type']));

       }

     }
}

If you want to go further you can write custom rewrite rules and add query vars to have those URLs be “pretty”.

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