Javascript stopped working while configuring routes

I am setting up this site with use of templates. 

Javascript files were functional and working welll, but as a was routing pages so that index.php would not show in the site url and setting up different pages this started causing problems with the javascript.

Controllers are similar to this: 

<?php
defined('BASEPATH') OR exit('No direct script access allowed');

class Services extends CI_Controller {

    function __construct() {
        parent::__construct();
   
        $this->load->helper('url');
    }

public function index()
{
$this->load->view('tjanster');
}
}
?>


all routes are: 

$route['om_oss'] = 'about';
$route['tjanster'] = 'services';
$route['offert'] = 'offert';

$route['pagaende_projekt'] = 'blog/pagaende';
$route['avslutade_projekt'] = 'blog/avslutade';
$route['ovriga_projekt'] = 'blog/ovrigt';

$route['default_controller'] = 'welcome';
$route['404_override'] = '';
$route['translate_uri_dashes'] = FALSE;



I assume that my javascript files are not running in the appropriate time. The site is https://engqvistwebb.se/dir/

Would love to get responses to this problem as i have been stuck here for ours. Probalby an easy solution to it.

Best regards
Joakim