use apply_filters return taxonomies custom post type

You forgot to add the existing taxonomies to the array you’re returning. try this:

function get_new_taxonomies ( $taxonomies) {

        return array_merge($taxonomies, get_object_taxonomies('my_custom_post_type'));
    }
add_filter('wp_taxonomies', get_new_taxonomies );

$wp_taxonomies_result = WP_Taxonomies::get_taxonomies();