Never had RC issues (right leg...whole other story but this thread is about you).
Regarding your trap bar shrugs, it very well could have contributed. The upper traps (what I presume you were targeting when doing shrugs) elevate the scaps. Most cases of RC problems involve weak scapular retractors (rhomboids, mid traps) and depressors (lower traps). Of course, you also need to strengthen the external rotators (teres minor, infraspinatus).
Although it's true the dead lift and trap bar dead will target the muscles I mentioned, if someone has a history of injury such as yours, they should most likely: 1) minimize strengthening of the overactive muscles (which, in your case, strongly appears to be upper traps) and;2) target the under utilized muscles directly (band work, W's, Y's, face pulls, etc.).