I experienced the same thing but on opposite legs. The problem was from not knowing how to keep my entire torso tight and stabilizing my hips. When squatting my knee on the side with the bigger tear drop would stay forward while the other knee would shift back. Once I learned to get everything tight and stabilize my hips, I've had an easier time controlling my knees. As a result their development has started to even out and I've experienced equal soreness in both sides and areas after every heavy workout.
The answer is to learn to brace your abs while getting your hip flexors and abductors involved throughout the movement. This will help you control hip position which in turn controls knee position.