Declare post types for Yoast's Orphaned Content filter (wpseo_orphaned_post_types)

functions.php

add_filter( 'wpseo_orphaned_post_types', 'set_wpseo_orphaned_post_types');
function set_wpseo_orphaned_post_types( $post_types ) {

	$post_types = array('');  // empty array disables the orhpaned content filter for all post types
	return $post_types;
}