This issue is new to beta 13, as far as I know.
At about 3PM, my time, I stopped Docked, deleted Docker.qcow2 and removed the log folder. They were about 95GB and 65GB, respectively.
Now at 5PM (two hours later), my hard drive is again filled.
$ du -sh *
Note: I have no idea why my Docker.qcow2 is so big, since I deleted it just two hours ago and now only have one image stocked and no containers running:
$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
alpine latest 13e1761bf172 2 weeks ago 4.797 MB
pinata diagnose -u
OS X: version 10.11.4 (build: 15E65)
Docker.app: version v1.11.1-beta13
Running diagnostic tests:
[OK] Moby booted