Override alter.inc in child theme
If you really want to remove bootstrap.js you can do it this way:

function YOURTHEME_js_alter(&amp;$js) {  
  $bootstrap = drupal_get_path('theme', 'bootstrap') . '/js/bootstrap.js';
  unset($js[$bootstrap]);
}


It might fix your menu plugin but it'll remove every drupal specific bootstrap js code (tabs, popovers, tooltips and anchors stuff).