Of Course, we all get it. It takes longer for ligiments to strengthen. Your muscles will get stronger and your knees hurt. Ride below you pain threshold as your knees (heal) stronger, thicker, and increased attachment area. Then you will feel good and go out and bust the hill. Oh! knees hurt again. We are talking aching knees. If you have Sharp pain that is injury and needs to be looked after.
The listless aching knees after a tough ride is your body grumbling about having to change. Eventually if you stay at it and listen to your body you become amazing, to yourself and others. I am not a Dr. but I ride free of pain and love the hills. Took me 6 years of mostly every other day riding. Sore legs, sore lungs, sore knees, all part of the journey. I feel I'm on a different level now and I like it.