In ALS, the muscles keeping the joint in place can get weak and place the joint at risk.
So, for example, in the example of the frozen shoulder (always a possibility, as Karen notes), some of the exercises used to heal it could strain some of those muscles past their ability to return to baseline, and even cause subluxation (partial dislocation) of the shoulder. This is a particular risk with ALS that started in the arms, esp. if they got really skinny at onset (flail arm type).
There is also some risk with exercise that you might do for tendonitis (another possibility, as you have seen), and even just normal range of motion work. In ALS, once subluxation occurs, it is unlikely you can get the joint back in place.
Essentially, you gently but firmly hold the shoulder in its socket while you manipulate the arm. So the therapist or CALS would be using two hands -- one to reconstitute the shoulder and the other to exercise the arm. At a certain point, based on progression, of course, you stop lifting the arm past the shoulder at all. Lying down is a good way ultimately to get as much exercise of the arms as possible, safely, as there is less strain on the joint at all. Even for PALS who are still somewhat mobile, exercise/massage in bed is a great way to start the day before the effort of transferring.
The same principle applies to knees, hips and elbows -- once you see atrophy or even before, you want to use the two-hand technique in passive ROM, but they are at lower risk, generally.