Using the W3TC plugin we found that it was possible for google to be indexing the CDN subdomain.
Here is what we did to help prevent the CDN subdomain from being indexed.
1) set the document root for the cdn subdomain to the following.
2) go to the document root directory.
3) set symbolic links to the original sites wp-content and the wp-includes directory.
ln -s /home/wpadmin/m3server.com/public_html/wp-content wp-content
ln -s /home/wpadmin/m3server.com/public_html/wp-includes wp-includes
These steps will prevent anything other then the sites content from working on the CDN subdomain.
Please see our post on how to setup W3TC plugin to work with our CDN services.
We also can show you how a cdn works.