pages get 404 but not the taxonomy page or home page

The code works like it should but the problem is that is breaks normal pages and gives med 404.php instead. Help please :/

home page [Works]: https://www.text.com/
taxonomy page [Works]:https://www.text.com/category/title
Normal pages [Error 404]:https://www.text.com/contact

function protocols_init() {
    $protocolsargs = array(
        'label' => 'label here',
        'public' => true,
        'show_ui' => true,
        'capability_type' => 'post',
        'hierarchical' => false,
        'query_var' => true,
        'menu_icon' => 'dashicons-admin-page',
        'menu_position' => 5,
        'has_archive' => true,
        'taxonomies' => array('primary', 'status'),
        'rewrite' => array('slug' => '%primary%'),
        'supports' => array('title','editor','author','thumbnail'),

    );
    register_post_type('protocols', $protocolsargs );

}
add_action( 'init', 'protocols_init', 0 );

function create_protocol_taxonomies() {

        $primarylabels = array(
            'name'              => _x( 'Categorys', 'taxonomy general name' ),
            'singular_name'     => _x( 'Categorys', 'taxonomy singular name' ),
            'search_items'      => __( 'Search Categorys' ),
            'all_items'         => __( 'All Categorys' ),
            'menu_name'         => __( 'Categorys' ),
        );

        $primaryargs = array(
            'hierarchical'      => true,
            'labels'            => $primarylabels,
            'show_ui'           => true,
            'show_admin_column' => true,
            'query_var'         => true,
            'rewrite'           => array('slug' => 'primary', 'with_front' => true)
        );

        register_taxonomy( 'primary', 'protocols', $primaryargs );

        // Add new taxonomy
        $statuslabels = array(
            'name'              => _x( 'Status', 'taxonomy general name' ),
            'singular_name'     => _x( 'Status', 'taxonomy singular name' ),
            'search_items'      => __( 'Search Status' ),
            'all_items'         => __( 'All Status' ),
            'menu_name'         => __( 'Status' ),
        'label' => __('Status')
        );

        $statusargs = array(
            'hierarchical'      => true,
            'labels'            => $statuslabels,
            'show_ui'           => true,
            'show_admin_column' => TRUE,
            'query_var' => 'status',
            'rewrite'           => array( 'slug' => 'status' )
        );

        register_taxonomy( 'status', 'protocols', $statusargs );
    flush_rewrite_rules();

}
add_action( 'init', 'create_protocol_taxonomies', 0 );

add_filter('post_link', 'primary_permalink', 10, 3);
add_filter('post_type_link', 'primary_permalink', 10, 3);

function primary_permalink($permalink, $post_id, $leavename) {
    if (strpos($permalink, '%primary%') === FALSE) return $permalink;

        // Get post
        $post = get_post($post_id);
        if (!$post) return $permalink;

        // Get taxonomy terms
        $terms = wp_get_object_terms($post->ID, 'primary');
        if (!is_wp_error($terms) && !empty($terms) && is_object($terms[0])) $taxonomy_slug = $terms[0]->slug;
        else $taxonomy_slug = 'not-rated';

    return str_replace('%primary%', $taxonomy_slug, $permalink);
}