The problem is in admin pages that abuse ext page id of other forms such as /admin/repositoryinstances.php which has PAGE->url pointing to admin/repository.php - I guess it would not be practical to forbid this common (but still incorrect) practice right now.

function admin_externalpage_setup($section, $extrabutton = '', array $extraurlparams = null, $actualurl = '', array $options = array()) {

The proper solution is to properly specify $actualurl in admin/repositoryinstances.php...