Alas, not all is well in Dockerland when it comes to CRIU. First if you’re using a 3.10 kernel like I did, you’ll find a lot of CRIU functionality doesn’t work. I had a hard time with “ghost files” and this specific issue.
So I started using an Ubuntu 16.04 LTS host (kernel 4.4.0-75-generic). This allowed me to install CRIU 2.6 which got me past the ghost file issue and I was able to successfully dump my container. However I then ran into issues when attempting to restore a checkpointed container. I have mounted filesystems in my container which CRIU and Docker in particular were unable to restore. This is documented in Docker issue 32227. The last 2 comments on that issue are pretty enlightening and if I knew Go, I’d fix it.