Files are being extracted at root level of docker layers

Docker version 17.06.0-ce, build 02c1d87
Operating System: Ubuntu 16.04 and Azure ACS

One of our docker images has been working perfectly with docker 17.05 and 1.13
After upgrading to 17.06 the image fails to run correctly with complaints about missing files

Connecting to the image, it appears that some files have been extracted into the root directory rather than their correct location lower down the file system. This appears to be confirmed by running
docker save -o out.tar clarity-channel-service

Error response from daemon: open /var/lib/docker/aufs/diff/af6f1d48a5cb51bde2a46b449f748be8e918c6082982ccfdfe772f3c183b42f1/opt/ISRM/AIT/channel-service/node_modules/rappid/node_modules/jointjs/demo/petri nets/src/smil.user.js: no such file or directory

Although I haven’t identified the root cause of the issue, this seems to be an issue with docker 17.06.0 extracting images created with docker 1.13. If I rebuild the same container using docker 17.06.0 everything works as expected.