Did the pain begin after you starting running or upped the distance? It could be a fallen arch. If your shoes aren't giving you enough support you can strain your plantar fascia which runs almost the length of the foot and the Posterior Tibial Tendon which helps hold up the arch. These can cause pain and or spasms on the bottom of the foot and the medial (inner) side of the ankle. 

Changing to new properly fitted shoes, or adding a shoe insert like (Superfeet) should relieve the stress.

Personal Trainer Hollywood - Los Angeles - Fitness