Hello

I had the same problem when I first started running. I had never ran before an after about two weeks my knees hurt on the inside and below knee cap. It sounds like you have runners knee, this can be caused from weak knees, training too hard too soon, walking unevenly on feet; which means you need stability shoes, not stretching your hamstrings properly and week thigh muscles.  What I had to do was quit running for a few weeks and ice my knees several time a  day plus I started using a good knee brace that would keep everything stable. Instead of running I started walking fast, using an ellipitcal and any other type of low or no impact excercise. I would recommend doing a search on the internet for runners knee, you will find all kinds of helpful information.

Hope this helps