Aaron Marino of alpha m. addresses a viewer question regarding sore joints from running. Increasing mileage takes a slow build-up. If not, your body will be beaten up by the end of the running.
Joints can hurt from shoes and overuse. Systematically build up mileage to be injury free. Glucosamine, chondroitin, MSN are supplements you can take for your joints. Running is tough on your body. Try cross training as well as methodically build up.