Docker taking much more space than sum of containers, images and volumes

I was having the same problem. I solved my problem by deleting log files

sudo sh -c "truncate -s 0 /var/lib/docker/containers/*/*-json.log"

Link: How to clear the logs properly for a Docker container?

You have two containers that are eating your storage. Those containers must be running, because you said you already ran docker system prune. Otherwise /var/lib/docker/containers would be empty.

So check why are those two consuming so much. Probably they are logging too much to stdout.