I'd challenge the frame of the question in that the imprecision of human communication and the difficulty of performing an exercise perfectly, might have led to confusion. In my experience, it's not terribly uncommon, when doing exercises, to recruit additional muscles for a particular exercise, particularly initially. This is perfectly normal, and part of normal function. In regular life, we don't isolate muscles to do things, but rather use our entire bodies. Of course, exercise is a more artificial situation where we are intentionally trying to do a movement less efficiently by attempting to do a movement in a more limited way to target specific muscles. What the doctor may have been intending to indicate was that you were recruiting additional muscles when attempting to push or resist movements, most likely using them to brace yourself more than trying to indicate that you were using them to actually move your arm.
So, why would this be relevant to your situation, specifically coming in to check function after an injury? Well, part of the natural adaptation after an injury is to use uninjured parts of the body to compensate for the injured parts, and the habit can remain afterwards, which can both make it harder to isolate a movement, and can also create additional fatigue when you continue to provide extra bracing when your arm is fully recovered. If you got into the habit of tensing your shoulder and back muscles before moving your arm in order to reduce pain and further injury, you may still be tensing them during movements, which will not only add additional energy expenditure, but also might work against the arm movement.
As to how you can counter this, the primary method is self-awareness. I'm probably not telling you anything you haven't heard before, but when exercising, it's important to be in the moment, to be aware of what your body is doing, and to not be too distracted. If you're watching a TV show, or listening to a podcast, it gets a lot easier to zone out and get into bad habits, like recruiting additional muscles or bracing yourself in unnecessary manners. For as much of the exercise as is possible, consider what your body is telling you about what muscles are being used. If you are not used to such self-introspection, you may be able to borrow another's senses by having a friend or spotter set their hand on areas where you're using the wrong muscles so that they can give you feedback if, e.g., you're heavily flexing your back muscles in an exercise where most of the movement should be in your arm.
