Counterup JS to work
Make sure all files are present !

The drupal way for custom js in your theme is a behavoir, so your js file should look like this:

    (function ($) {
      Drupal.behaviors.myThemeBehavior = {
        attach: function (context, settings) {
           $(context).find('.counter').once('myThemeCounter').counterUp({
             delay: 10,
             time: 1000
           });  
        }
      };
    })(jQuery);


This will ensure the script is executed after the DOM is loaded and only will run once.