One of the concepts of the Matrix training theory is with increased size and strength gained in resistance training ever larger stresses are applied during that training without much commensurate increase in recovery capacity. You can develop muscular strength and generate higher levels of intensity at a much higher rate than you can increase your ability to tolerate it. In other words, if you consistently follow one fixed training routine and grow stronger over time, chances are that you will eventually burnout and over train. So, the first rule to follow is to periodize or cycle your training to allow your overall system a chance to recover and compensate. During low intensity cycles, your recovery abilities can be fortified including your immune system. During high intensity cycles, you stress your recovery abilities to the limit, "pushing the envelope" so to speak, and stimulating new muscle growth. You need cycles of both to progress consistently. The Matrix programs periodize your training efforts, which gives your body a chance to recover appropriately between intense efforts. If you don't plan low intensity cycles in your workouts, your body will do it for you by catching that unsuspecting cold, pulling a muscle or straining a joint.
Another main issue is muscle training frequency. Our routines are designed to stimulate specific body parts individually and together. An effort is made to avoid exercises, which overlap or indirectly stimulate the same muscle groups over and over again. Overlapping movements will tend to stress the same muscles too extensively and possibly too often leading to training plateaus and overtraining. An example would be to aggressively train the chest on Monday, the shoulders on Wednesday and the triceps on Friday. There are too many overlapping muscle groups involved in all three workouts to make any significant progress.
In many cases we see most of the overlap between upper body movements. Which means the upper-body is generally trained twice as frequently as the lower body. Thus, lower body training may often be low frequency and low volume while upper body training is high frequency and high volume. Its interesting to note that most of the trainees we consult initially report faster gains in their legs compared to their upper bodies. By far, the upper body parts most subject to over-training through such double dosing are the shoulders and arms. It is simply impossible to do any upper body movement without involving these two bodyparts. Moreover, its obvious that some of the best movements presumably for one body part are excellent movements for other body parts as well. Thus, dips "performed for triceps" are excellent for chest and shoulder development and pull-downs performed for upper back are excellent for biceps and forearms. Its easy to see that using less upper body exercises and focusing on compound movements can be a beneficial strategy for anyone weight-training.
Take a look at your program and try to identify where the overlapping movements occur and decrease their frequency or eliminate them altogether. Train both the deltoids and arms at a lower volume than the rest of your torso since you know they're involved in all your other upper body movements. You'll have to take a step back in your thinking in order to take two steps forward in your physical development.