Bootstrap theme overrides "theme_list_item" function and removes div's "item-list" class
1) Default markup. To return default item list markup just do this:

function bootstrap_subtheme_item_list($variables) {
  return theme_item_list($variables);
}


2) But. Your issue is not caused by Bootstrap markup. Try this:

$form['header'] = array(
  '#markup' =&gt; $stages_list,
);


You are using fieldset incorrectly, learn Form API Reference.