The following line will not work as you provide and url as filename:
$zip->addFile('qr_gen.php?criteria=1', 'alpha.png');
Instead you'll have to download the pngs first and store them locally. Then add them to the zip archive. Like this:
file_put_contents('alpha.png',
file_get_contents('http://yourserver.com/qr_gen.php?criteria=1');
$zip->addFile('alpha.png');
You'll find more information at the documentation page of ZipArchive::addFile()