Klian

Same error here with WP 4.9.8 and Yoast 7.9

The problem is that the save_post action doesn’t fired up with the edit attachment page… so we have to add a new action to execute it.

I’ve fixed it editing cpt-onomies/admin.php file:

Below line 52:
add_action( 'save_post', array( &$this, 'save_post' ), 10, 2 );

Add this:
add_action( 'edit_attachment', array( &$this, 'save_attachment' ), 10, 2 );

At the end of the file add this function:

public function save_attachment($post_id){
		global $cpt_onomies_manager, $cpt_onomy;
		// pointless if $_POST is empty (this happens on bulk edit)
		if ( empty( $_POST ) ){
			return $post_id;
		}

		// verify nonce
		if ( ! ( isset( $_POST[ 'is_bulk_quick_edit' ] ) || ( isset( $_POST[ '_wpnonce' ] ) && wp_verify_nonce( $_POST[ '_wpnonce' ], 'update-' . $post->post_type . '_' . $post_id ) ) || ( isset( $_POST[ CPT_ONOMIES_UNDERSCORE . '_nonce' ] ) && wp_verify_nonce( $_POST[ CPT_ONOMIES_UNDERSCORE . '_nonce' ], 'assigning_' . CPT_ONOMIES_UNDERSCORE . '_taxonomy_relationships' ) ) ) ){
			return $post_id;
		}

		// check autosave
		if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ){
			return $post_id;
		}

		// dont save for revisions
		if ( isset( $post->post_type ) && $post->post_type == 'revision' ){
			return $post_id;
		}

		$post = get_post($post_id);

		// check cpt-onomies

		foreach( get_object_taxonomies( $post->post_type, 'objects' ) as $taxonomy => $tax ) {

			// make sure cpt-onomy was visible, otherwise we might be deleting relationships for taxonomies that weren't even "editable"
			if ( isset( $_POST[ 'assign_cpt_onomies_' . $taxonomy . '_rel' ] ) && $cpt_onomies_manager->is_registered_cpt_onomy( $taxonomy ) ) {

				// check permissions
				if ( ! current_user_can( $tax->cap->assign_terms ) )
					continue;

				// set object terms
				if ( isset( $_POST[ CPT_ONOMIES_POSTMETA_KEY ][ $taxonomy ] ) ) {

					// need to make sure its an array
					if ( ! is_array( $_POST[ CPT_ONOMIES_POSTMETA_KEY ][ $taxonomy ] ) )
						$_POST[ CPT_ONOMIES_POSTMETA_KEY ][ $taxonomy ] = explode( ',', $_POST[ CPT_ONOMIES_POSTMETA_KEY ][ $taxonomy ] );		

					$cpt_onomy->wp_set_object_terms( $post_id, $_POST[ CPT_ONOMIES_POSTMETA_KEY ][ $taxonomy ], $taxonomy );

				}

				// delete taxonomy relationships
				else
					$cpt_onomy->wp_delete_object_term_relationships( $post_id, $taxonomy );

			}

		}
	}

This method works for me.