My knees sidetracked me for a bit, also in week 3 I think. Tight IT bands and weaker inner quad muscles (Vastus Medialis?) resulted in my kneecaps getting pulled outwards a bit. That caused clicking and some pain, but mainly a feeling like they were going to give out on me. I went to physical therapy. My PT taped my knees to align them and keep them stable (not like any of the taping instructions I've seen online though) and that helped immediately. I did lots of stretching using a foam roller on my IT bands and did exercises and had some electric stimulation treatments to strenghen the inner quad.

If you think your knee problem sounds similar (kneecaps point and are located a little outwards) one of the quad exercises was really easy. When you're sitting with your feet slightly in front of your knee, push your heel into the ground. If you put your hand on your inner quad near the knee you should be able to feel the muscle contract. It's easy to do at different times throughout the day.

If it continues (and you can afford it), I'd really recommend a trip to a PT to pinpoint what's really wrong. Good luck!

I have the beginnings of arthitis in my knees, and I found it best to strengthen the muslces around the knee. So I take the stairs more often and strength train my thighs, calves, hammies, etc. That has helped a lot. After a run, my knees sometimes will feel sore, but I just think of that as a confirmation that I did a good job