Until Docker native can automatically do this, use this script to reclaim free space from your Docker.qcow2 file.

docker-shrink

#!/usr/bin/env bash

set -e
set -o pipefail

function qcow2_size() {
    wc -c Docker.qcow2 | awk '{print $1}'
}

cd ~/Library/Containers/com.docker.docker/Data/com.docker.driver.amd64-linux
echo "Bytes before shrink: $(qcow2_size)"
/Applications/Docker.app/Contents/MacOS/qemu-img convert -O qcow2 Docker.qcow2 Docker2.qcow2
mv Docker2.qcow2 Docker.qcow2
echo "Bytes after shrink: $(qcow2_size)"