This sounds like the same issue that I encountered recently for post types that did not have an archive page. I believe the issue was introduced with the release of version 6.1.4 of the plugin. If you check your CloudTrail logs and see “://*” listed among the invalidation paths in the request, then that is likely the problem. I submitted a pull request to the plugin’s GitHub repo to address this.
https://github.com/amimoto-ami/c3-cloudfront-clear-cache/pull/108
