Jetpack API for WordPress Network

I answered my own question.

The slash in the URL messes up the API call. However urlencoding the URL will get around it.

IE:

$context = stream_context_create( $options );
$site = urlencode("subdomain.example.com/site1");
$response = file_get_contents(
'https://public-api.wordpress.com/rest/v1/sites/' . $site ."https://wordpress.stackexchange.com/",
false,
$context
);