Pain is usually a good indicator that something isn't quite right and its time to slow down a little. Ice the area of pain - when did you notice the pain? Was it during the run? After the run? If during the run did it come on gradually and get worse?
There are a couple of things it could be such illiotibial band friction syndrome (ITBS) or paetella femoral pain (PFP) have a look at
www.physioroom.com. As you said you had pain going upstairs I was assuming the latter but you'd need to see a trained professional for a proper diagnosis.