OK, got it. This is not a multi-site issue, but a bug nonetheless with %20 in CSS URL's not being converted into spaces when trying to get the path.
Could you open up /wp-content/plugins/autoptimize/classes/autoptimizeBase.php and in the getpath()-function on line 27 change;
protected function getpath($url) {
if (strpos($url,'//')===0) {
into
protected function getpath($url) {
$url=urldecode($url);
if (strpos($url,'//')===0) {
If that works, I'll add it to the upcoming 1.9.0 which I'm working on.
frank