I doubt that's cycling-related other than incidentally. Looks like maybe a bone spur rubbing a tendon. See an orthopod (orthopedic surgeon). Could also be an ankle sprain. Get it looked at anyway. Not a good look.

SPD pedals have plenty of float. You can check, though. While riding, fool with twisting your feet. You don't want to be up against either stop, rather somewhere in the middle of where your feet want to be. If that's not true, adjust your cleats until it is.