Personally, my biggest gripe with Dockerhub is that a Dockerfile should be required in order to upload to the hub, and it should show the Dockerfile that produced each version. The fact that people can create fundamentally unreproducible binaries is nasty (there's also the issue of not specifying versions in the apt/yum steps used in the Dockerfiles, but that's just a general problem with the way package management software is designed).
None of that's a problem with Docker itself though.