I've had some issues with this as well. I noticed my legs are slightly different so I need to consciously make the effort to point my right leg in the right direction and make sure my toes are pointing outwards/straight. Just get a feel for where your knees want to be and where they need to be and try to allow them to stay in form through the ride.
Also: shoe tightness. keep both shoes the same tightness or you push harder with one leg, over loading the knee.