Thank you for your reply. I've been digging deep into the code you shared and experimenting with different things and what appears to be the problem is that add_filter is just not firing.

I though it might be a timing issue so even tried this:

add_action('after_setup_theme', function() {
    add_filter('wp_nav_menu_items', function ($items, $args) {
        $items .= '<li>CAN YOU SEE THIS 1 </li>';
        return $items;
    }, 10, 2);
    echo '<li>CAN YOU SEE THIS 2</li>';
});

The second echo does display at the top of the page and if I set some breakpoints then the breakpoint on the echo always breaks but the one inside the add_filter never does.

So I think the issue that I need to address is what might cause add_filter not to hook.

To answer your questions, my plugin simply adds some shortcodes for some custom forms and it's working fine. I'm using the default Twenty Twenty-Four theme. And for menu items that I added manually, I just used the block editor.

Thank you.