Docker is a trend and everyone want to be part of this but not really in a good way. The bad side of this trend is that everything goes on container, like web app or database even GitLab to the detriment of data persistence, security and maybe performance in in certain case.
One of a solution is, IMHO, to use a orchestrator like Swarm or Kubernetes with a good study of which kind of volumes all your containers need. You can also make security better with a good reverse proxy and using RBAC for Kubernetes.
What is your methods to keep your data safe, to make container secure and to have good performances on your conteneurized website ?