Weird knee rotation and pain

I was a gymnast 50+ years ago when I was your age. Back then we didn't have the padded mats and harnesses they use today to reduce impact on knees and hips, but at that age the pain and discomfort was bearable and disappeared after a while.The years of gymnastics came back to haunt me in my late 50's and increasing chronic pain caused me to have the first knee replacement in May. 2017. Post op complications landed me in a wheelchair for 7+ months and it is only now I am starting to practice walking with crutches. My right knee replacement will have to wait until I see how the left leg recovers. Some of my fellow gymnastic team mates also have knee and hip problems now. Where we once moved with strength and grace, we now struggle to stand and walk.

Moral of the story- stress and abnormal movements in youth can come back to haunt you when you're older. Pain is one way the body tells you not to do something. From what you describe, you may be risking your mobility in the future doing what you're doing now. 

You need to talk to a sports medicine orthopedic surgeon. He has probably seen the same thing before and may want some diagnostics done before offering his opinion and suggested remedy. Knees are difficult to self diagnose as we are all so different in our daily activities. One concern with just letting it ride or guessing, knee problems generally worsen rather than self heal. If you are going through a period of substantial growth both in height and weight, a year may make a difference but on the safe side, a qualified Dr s opinion will remove the anxiety and may get you some relief. Ask your coach if he knows a qualified Dr or sports med physical therapist. The PT might be easier to get I to and could offer suggestions.

I think it may be the muscular pain which you are facing  and as you are a  sportsman you have great stamina but in my opinion I should suggest you should consult with specialist to get better consultation and treatment for your knee pain.