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Beginning a new exercise program can have set-backs early on as the body is adjusting to the routine. Any pain in the foot and/or ankle of a runner is an indication that it is time to rest and evaluate the situation. Problems that gradually come on a month or so after starting an exercise can be minor or a sign of a more serious foot condition. A reassessment of the exercise regimen (warm-up, hills, speed, etc.) and proper footwear can minimize foot injury. It is generally best to wait until all pains are gone prior to reinstitution of exercise. If pains persist in spite of resting, an evaluation by a qualified medical professional should take place. There are many injuries that can cause the symptoms that you describe, ranging from ligament strain and tendinitis to stress fracture (a small crack) of the bone.
Thank you for your question and I hope you can enjoy your exercise again soon.