Open two terminals, in terminal one run

docker run -it --name bad ubuntu bash

In terminal two run

docker exec -it bad bash

In terminal one, hit CTRL-D, killing the terminal. Now you run

docker stop bad

And you get

Error response from daemon: Cannot stop container bad: no such process FATA[0000] Error: failed to stop one or more containers

You can't get rid of container "bad" until you restart Docker. I tried this in Docker 1.3.3 and could not reproduce.