Reading through your question, your submenu is on
add_filter('nav_menu_css_class' , 'special_nav_class' , 10 , 2);
function special_nav_class ($classes, $item) {
if (in_array('current-menu-item', $classes) ){
$classes[] = 'active ';
}
return $classes;
}
it would be more easy to figure-out the error, if you can share your code and screenshots. Hope this will solve your issue