Issues with IE11 and Caching

I don’t know why, but some pages of my website are not working using the Internet Explorer 11. Looking into the source code and comparing the working and non-working pages, it seems like an essential js file is not being loaded (it’s a polyfill which does serve as a fallback for the IE. It is working fine, until W3 is activated).

I’ve enqueued the polyfill js file like this:

function mysite_enqueue() {
    $ua = htmlentities($_SERVER['HTTP_USER_AGENT'], ENT_QUOTES, 'UTF-8');
    if (preg_match('~MSIE|Internet Explorer~i', $ua) || (strpos($ua, 'Trident/7.0') !== false && strpos($ua, 'rv:11.0') !== false)) {
        wp_enqueue_script(
            'polyfill',
            get_stylesheet_directory_uri() . '/js/polyfill.min.js',
            array(), '1.0', true
        );
    }
}
add_action( 'wp_enqueue_scripts', 'mysite_enqueue' );

Could this be the issue? After clicking “purge all caches”, the site is working for maybe like an hour. After that, it is broken again. Strangely some pages work and some not.

My W3 Total Cache plugin settings are mostly default. JS minification is disabled.

Thanks for any help!