Try adding preserveWhiteSpace = FALSE;
to DOMDocument object where is file stored.
$xml = new DOMDocument('1.0', 'utf-8');
$xml->formatOutput = true;
$doc = new DOMDocument();
$doc->preserveWhiteSpace = false;
$doc->loadXML(file_get_contents('data.xml'));
$doc->formatOutput = true;
...