I changed the line in the file inc/classes/BxDolTemplate.php:

    if($sUrl)
      $sRet .= '<link rel="canonical" href="' . $sUrl . '" />';

to the version from UNA 14:

    if (!empty($this->aPage['url'])) {
      $sRet .= '<link rel="canonical" href="' . bx_absolute_url(BxDolPermalinks::getInstance()->permalink($this->aPage['url'])) . '" />';
    }

It seems that now all links are correct. But I don't know how right this solution is.