I think if you had a rotator cuff injury (or any shoulder injury) that you would feel pain during other movements, especially overhead pressing and bench pressing.
No matter which bar position you use, high bar or low bar, you should not have bruising or pain. The bar should rest on your muscles (upper traps and rear delts), never on your spine (high bar) or the spine of your scapulae (low bar).
Here's an excellent instruction video on bar position. Hopefully it will help you determine what is going on in your own situation.
Squat Rx #4 - Bar Positioning and Squat Depth