add_filter( 'wdp_save_cart_item_keys', function ( $keys ) {
 $keys[] = 'original_item';
 return $keys;
} );

add_filter( 'wdp_skip_cart_item', function($skip, $item, $product) {
    if( isset($item['original_item']['bundled_by']) ) //ignore product inside bundle
        $skip = true;
    return $skip;
},10,3);