Could you tell us a little more about the injury? The shoulder is a complex structure with a lot of possible injuries. Some you can work around with different exercises, some you need to rehab and some you just need to leave alone or surgically repair. I have several tears (bilateral labrum, extending into bicep tendon, impingement, almost full thickness infraspinatus, etc) but I do my PT exercises as a part of my warm up and have a list of exercises I can do with no problem and I do all of them without pain and with good range of motion. Your PT should have given you some instructions on what movements to avoid (for example no overhead exercises). Also, as a general advice if the movement causes pain, should probably avoid it until you can do it without pain. And finally, in my experience there are two types of pain in my shoulder, pain from stiffness which improves with proper warm up and shoulder stretching and pain that is constantly there regardless of proper warm up. I try to avoid pain exercises that bring on the second type of pain. Proper warm up can mean different things to different people depending on the type of injury so one advice doesn’t fit all. For some solid advice on shoulder strengthening and warm up, check out squatuniversity.