As is usually the case, your physiotherapist is full of shit. The only way a "wide-stance" squat can cause patellar tracking problems is if the femur and the tibia are aligned wrong, i.e. your feet are not in line with your femurs. This means that the wider the stance, the wider the toe-point must be. If this alignment is respected, all the quadriceps work evenly to extend the knee. The advantage of my "wide-stance" squat is that it also works the adductors, left out by close-stance squats. Does you physiotherapist know that adductors are involved in the squat?
As for your hip injury, it could be the hip joint, or it could be the trochanteric bursa, under the glute insertions on the top of the outside of the femur, and not really a hipjoint problem. Where is the pain? Exactly?