I doubt that it is he doctor giving him fake vivitrol, there is little to no incentive for someone to counterfit it and tons of regulations that would make it very difficult to. There isn't a black market for the drug that I am aware of either, so it would almost have to be the drug companies making weak or bad product.
It's far more likely that there is something going happening on a physiological level in your son. A few questions come to mind: was he completely sober/detoxed off heroin before the treatment began? If so, can you be 100% positive that he wasn't using at all prior to the treatment, because it sounds like he is still hiding his behavior.
Are you sure that he only used twice? And only the amounts specified? Even 2-3 bags sounds like a lot of dope to be doing without a tolerance. I'm pretty sure you can still OD, you just won't get as high. He's playing a very risky game by using.
Also, I don't really understand how you would be able to feel it wearing off unless you are doing dope on a regular enough basis to notice the difference. Basically it binds to the same areas of the brain that opioids bind tom but instead of causing stimulation it has a reverse effect. But I've never taken it personally so I can't say for certain.
Have you spoken with the doctor and counselor? What do they have to say? Chances are the counselor might have a little better insight to the situation. It can be difficult to know what to believe when it is someone so close. I'm sure you want to believe and trust your son, but the hard truth is that drugs can change people and cause the user to do things even he/she wouldn't expect.