Indirect modification of overloaded property WP_Post::$classes has no effect

If “line 45” is the one that starts with $element->classes[] in your display_element method then try something like this:

public function display_element( $element, &$children_elements, $max_depth, $depth = 0, $args, &$output ) {
    $element->has_children = ! empty( $children_elements[ $element->ID ] );

    if ( ! isset( $element->classes ) ) {
        $element->classes = array();
    }

    $element->classes[]    = ( $element->current || $element->current_item_ancestor ) ? 'active' : '';
    $element->classes[]    = ( $element->has_children && 1 !== $max_depth ) ? 'has-dropdown' : '';        

    parent::display_element( $element, $children_elements, $max_depth, $depth, $args, $output );
}

The problem may be that the display_element function receives an element that doesn’t have that classes property set in which case you are trying to push data to an array that isn’t referenced anywhere except that instance only.

EDIT: Also, why are you using the display_element function when you can insert those classes in the start_el function which itself gets called by display_element with that element passed to it?

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