How to add multiple value using autocomplete widget
You need to explode the string inside the autocomplete function. 

function autocomplete_callback($string) {
  $explode_str = explode(',', $string);
  $last_str = drupal_strtolower(array_pop($explode_str));
  // use $last_str in the query
  $explode_str[] = $result;
  return implode($explode_str);
}