It is not unusual for large puppy dogs to get skeletal/ligament problems especially if they experience rapid growth (e.g. panosteitis). Injuries at an early age can also cause reoccurent problems.

If your dog is not a fast growing large type, then you have to ask if the breed (or breeds if mixed) are genetically prone to skeletal problems (e.g. luxating patellae).

Most likely you have a soft tissue injury that was reaggravated by too much exercise. Have the puppy Xrayed just in case. Chances are the Vet will prescribe a NSAID drug to help relieve the inflamation and pain. The treatment should be kept short term if possible to avoid liver problems. Avoid aspirins unless you use an acid blocker first. Aspirin can really cause ulcer problems quite easily in dogs.