Is it normal to have knee pain after running on a treadmill?

Hello doctor,

I recently started running (treadmill), but after a week or so, I found that my knees were really hurting. I continued thinking it was muscular, but it got to the point at which I was in a lot of pain. I stopped running and it has taken three weeks for my knees to feel almost normal. I had extreme pain behind the outside of my right knee, making it difficult to bend, and pain on the inside of both knees, which still feel bruised to touch, as well as at the top of both the calf.

I have long legs and my feet lean inwards. Could this be what caused the problems? My concern is that if I start running again, the same thing will happen. I do not want to train for two weeks and then have to take three weeks off due to being almost unable to walk. I wondered if perhaps some people just really really should not run, and that there is alternative cardio I should do? Just as a note, I have been doing resistance training for a year and so I assumed that my leg muscles were quite strong.