As noted, persistent pain is not good, but if your knees have to hurt, then an ache is much better than sharp, searing, or shooting pain or obvious swelling. An ache is more likely to be a mild situation due to overuse and may indicate that healing and strengthening is in progress. If you don't experience improvement and are still using NSAIDs (e.g. aspirin, Tylenol, ibuprofen) after a week, you should definitely see a doctor in my opinion.

P.S. That ache is also a signal to lighten up your pack or your body weight or both, if you can.