The external plantar nerve crosses the foot about 1-2 inches below the front of the ankle on the top of the foot. Its quite common to bruise the nerve in that area as the nerve is very close to the surface. I quite commonly get pain in this area usually when I've had my shoes too tight. Try running in a different pair of shoes or with thicker socks you may find this provides sufficient protection for the nerve. That would be my guess anyway.