In your image (http://docs.bluerobotics.com/fathom-s/pixhawk-setup.png) on the Fathom s’s documentation page you show a cable from the Fathom S to the Pixhawk. I have a cable that looks like the one in the image and both ends of the cable plug into the Pixhawk fine. However neither end plugs into the Fathom S.
This is a strange situation that you are explaining. There is a DF13 connector on the Fathom S board, what is your problem with it? Can you show us pictures demsonstrating the problem?
You may be using a pixhawk clone and a cable with a picoblade connector, which is different than a DF13.
If you don’t mind a little deformation, a bit of brute force (aka hacking ) will usually make two work together. Trimming some plastic off the edge of the connector can help.