Clear the cache/cookies and retest. Have them try a different browser/device. Make sure you restart the webserver and PHP-FPM (if you're running it) to clear any file cache. If you use a shared host ask them if there is anything else you need to do to clear any file cache. Most of the time PHARs are heavily cached so even if you replace the PHAR file it will still serve the cached version.
Other than that look into your logs on the AD server to see if their authentication attempts are actually going through and if they are successful or not.
Cheers.