I run into this pretty frequently with Docker on Mac OS X. Passing the `--rm` flag helps, but for cleaning up old/unused containers, I usually set these two commands on a cron:
# Remove un-tagged or un-named images
for im in $(docker images | awk '/<none>/ { print $3 }'); do docker rmi $im; done
# Remove stopped containers
docker rm $(docker ps -a -q)