debugging js scripts

What you might do is check the status of the scripts you are trying to enqueue after doing so.

Also, be sure to enqueue things inside of an action.

e.g.

function do_my_enqueue_scripts() {
   wp_register_script('isotope', get_template_directory_uri() . '/js/jquery.isotope.min.js',array('jquery'),'',true);

   wp_enqueue_script('isotope');
}
add_action('wp_enqueue_scripts', 'do_my_enqueue_scripts');

You can use the wp_script_is function to check if they actually get enqueued.

e.g. after

wp_enqueue_script('isotope');
if ( ! wp_script_is('isotope', 'enqueued') ) {
    echo '<p>Script failed to queue up!</p>';
}