Docker will autostart any container with a RestartPolicy of 'always' when the docker service initially starts. You'll have to dig into the container configuration to find it.
docker inspect my-container (Look for RestartPolicy in the output)
I've mostly had this situation occur when a container was created with --restart always, and the situation later changed such that I no longer wanted this to happen.
After docker 1.11, this is easy to fix
docker update --restart=no my-container