Page Not Found Old CSS References
You should do a search of the entire codebase (not just theme files), as well as a database search in all tables (it should only take about 3 minutes).

UPDATE:

Also, make sure you have taken any content delivery network (CDN) caching into account. Are these files causing "File-not-found" errors from a remote browser, or from a browser on the local machine (dev laptop, for instance).

If you do have a CDN in place (MaxCDN, CloudFront, Akamai, etc.) you can try uploading a mostly blank CSS file with the same name as the one that you're attempting to get rid of.