Last query_var not working with rewritten URL

[] = not [] .= to append to an array.

function custom_query_vars_filter($vars) {
  $vars[] = 'ae_issues';
  $vars[] = 'issueloc';
  $vars[] = 'issuearea';
  return $vars;
}

Another trick, if you don’t want to mess with a query is to change these vars to something like _issueloc & _issuearea. I found making custom queries as flags is nice for template redirects but not necessary to mess with the main query (unless you require it).

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WORKING

An alternate might be to added using add_rewrite_tag().

add_action( 'init', function() {
    add_rewrite_tag( '%ae_issues%', '([^/]+)' );
    add_rewrite_tag( '%issueloc%', '([^/]+)' );
    add_rewrite_tag( '%issuearea%', '([^/]+)' );

    add_rewrite_rule( '^issues/([^/]+)/([^/]+)/([^/]*)', 'index.php?ae_issues=$matches[1]&issueloc=$matches[2]&issuearea=$matches[3]', 'top' );
    add_rewrite_rule( '^issues/([^/]+)/([^/]+)', 'index.php?ae_issues=$matches[1]&issueloc=$matches[2]', 'top' );
} );

add_filter('template_include', function($template){

    global $wp_query;
    if( isset($wp_query->query_vars['ae_issues'])) {
        echo "<pre>";
        print_r($wp_query->query_vars);
        wp_die();
    }
    return $template;

});