One change in the latest version to how the CDN (with AWS S3) is controlled on a multisite install is that by default it requires you to use a single bucket. That's good news for us, but the problem is that it sends the files into <bucket_name>/files for all sites. So if we have images with the same name on different multisite installs one of the files gets overwritten.
Two ways I can think to fix it:
1) start from blogs.dir when uploading to the CDN and include the blog ID as the top level folder.
2) allow us to specify a bucket name (or top level folder) in the CDN config for each blog.