It is absolutely possible to have knee pain that results from muscular imbalance/weakness. I had knee pain which was caused by a tight/irritated IT band which was caused by a weak/irritated piriformis. That is one of the minor gluteals which rotates your thigh. Since we cyclists are super strong forward and back, but tend to be weak side to side, it's more prevalent among cyclists than normal people.
It was treated with PT (stretches, elastic bands, and other exercises) and ibuprofen. But the best thing I started doing was playing rec league soccer. Haven't had any pain since.