I had a doctor tell me I had arthritis in my knees several years ago before I turned 30. For me, I found that I have to be very proactive in stretching my thighs and using a massage stick on the quads. When my quads get tight, they pull on my knee cap and tendons and such and give me quite a bit of discomfort. As long as I keep everything lose, pliable and feeling good-- my joints feel great. I squat heavy every day by the way too.
Not saying this is your fix, but a lot of discomfort that I have experienced has been caused by tightness or imbalance in my body. When I address these things, my body feels good.