I'm getting quite frustrated setting up the correct URL structure for a CPT with a custom taxonomy.

I have a CPT called 'courses' with a custom taxonomy called 'course type'. The url structure should be: site.com/courses/course-type/course-single-post. For example: site.com/courses/science/rocket-to-the-moon/

I've managed to achieve that however not all URL parts are behaving as it should.

site.com/courses/ returns a 404

site/com/courses/science/ shows an archive page with all posts in side that custom taxonomy which is correct

site.com/courses/science/rocket-to-the-moon/ shows the single CPT which is correct too

Thing is , I don't know why the site.com/courses returns a 404 instead of showing an archive page listing all CPT's...?

This is the code that I've used:

<?php 

/*Courses Custom Post Type*/
function my_custom_post_courses() {
$labels = array(
    'name'               => _x( 'Courses', 'post type general name' ),
    'singular_name'      => _x( 'Course', 'post type singular name' ),
    'add_new'            => _x( 'New course', 'reis' ),
    'add_new_item'       => __( 'Add new course' ),
    'edit_item'          => __( 'Edit course' ),
    'new_item'           => __( 'New item' ),
    'all_items'          => __( 'All courses' ),
    'view_item'          => __( 'View courses' ),
    'search_items'       => __( 'Search courses' ),
    'not_found'          => __( 'Nothing found  ' ),
    'not_found_in_trash' => __( 'Nothing found in the trash' ),
    'parent_item_colon'  => '',
    'menu_name'          => 'Courses'
);
$args = array(
    'labels'        => $labels,
    'description'   => 'Enter a new course',
    'public'        => true,
    'menu_position' => 5,
    'supports'      => array( 'title', 'editor', 'thumbnail', 'excerpt', 'comments' ),
    'has_archive'   => true,
    'hierarchical'  => true,
    'rewrite'       => array('slug' => 'courses/%course-type%','with_front' => false),
    'query_var'     => true,
    //'rewrite'     => true,
    //'publicly_queryable' => false,
);
register_post_type( 'courses', $args );
}
add_action( 'init', 'my_custom_post_courses' );

/* Courses custom taxonomy */
function my_taxonomies_course_type() {
$labels = array(
    'name'              => _x( 'Course type', 'taxonomy general name' ),
    'singular_name'     => _x( 'Course type', 'taxonomy singular name' ),
    'search_items'      => __( 'Search course types' ),
    'all_items'         => __( 'All course types' ),
    'parent_item'       => __( 'Parent course type' ),
    'parent_item_colon' => __( 'Parent course type:' ),
    'edit_item'         => __( 'Edit course type' ),
    'update_item'       => __( 'Update course type ' ),
    'add_new_item'      => __( 'Add new course type' ),
    'new_item_name'     => __( 'New course type' ),
    'menu_name'         => __( 'Course type' ),
);
$args = array(
    'labels' => $labels,
    'hierarchical'  => true,
    'public'        => true,
    'query_var'     => 'course-type',
    'rewrite'       =>  array('slug' => 'courses' ),
    '_builtin'      => false,
);
register_taxonomy( 'course-type', 'courses', $args );
}
add_action( 'init', 'my_taxonomies_course_type', 0 );

/* Permalink filter Courses */
add_filter('post_link', 'course_permalink', 1, 3);
add_filter('post_type_link', 'course_permalink', 1, 3);

function course_permalink($permalink, $post_id, $leavename) {
if (strpos($permalink, '%course-type%') === FALSE) return $permalink;
    // Get post
    $post = get_post($post_id);
    if (!$post) return $permalink;

    // Get taxonomy terms
    $terms = wp_get_object_terms($post->ID, 'course-type');
    if (!is_wp_error($terms) && !empty($terms) && is_object($terms[0]))
        $taxonomy_slug = $terms[0]->slug;
    else $taxonomy_slug = 'no-course-type';

return str_replace('%course-type%', $taxonomy_slug, $permalink);
}