So you're claiming that even where the methodology is faulty, if it differently faulty in an individual case then the person under study must be suspicious?
I don't think you really understand the "faulty" part in "faulty."
Was it faulty methodology, or just unconventional and different? As far as I know (I watched the show) it seemed like a reasonable test that is used for other purposes as well.
And yes, suspicion must be cast. Remember dieselgate? Just because VW cars passed under the standard test meant they passed under a different test. In fact, it was the fact that the test results of the different test didn't line up that caused people to wonder what was happening. And it turns out in the end that the results were being gamed - when the car detects it was being tested, it cheated.
Want another one? Melamine in milk. Chinese farmers were watering down the milk. But if you do that, they can tell because the milk protein concentration goes down as well. So they added melamine to the milk, which resulted in the measured milk protein to be back to normal.
It's entirely possible that Subway is innocent. But it's also just as likely they're cheating. They're well known to abuse their "we're a healthier alternative" to offer pretty lousy food. Heck, for a long time, their "brown bread" (or "whole wheat") actually was white bread colored brown (by the same CBC folks, too). They analyzed the ingredients, and enriched WHITE flour was the first on the list. They found additives like caramel, molasses and others were added to color the bread brown. (Yes, they added a few whole grains in there, after the fact). The reason people found out was diabetics were wondering why after eating a "whole wheat bread" sub from Subway, their blood glucose readings spiked dangerously high - turns out their "brown" bread was basically sugared white bread.