This might be tempting, because the author does cite evidence in favor of her claim. But this evidence doesn't undermine the accuracy of the evidence advanced for the opposing position. The author isn't saying that people are wrong when they claim to have experienced acne after eating more chocolate. She is providing an alternative explanation for why those experiences occurred, but not necessarily denying that those experiences occurred in the first place.

This is correct. The additional evidence is the recent studies showing that stress can cause acne, and the evidence showing that stress can cause people to eat more chocolate. This information suggests an alternative interpretation of why many people susceptible to acne claim to experience acne after consuming large amounts of chocolate, which is the evidence provided for the "common wisdom" position. The author's additional evidence suggests that the reason these people experience the two phenomena together is not that eating chocolate itself causes acne, but because both are the result of stress.

While the author does point to scientific evidence in response to a position for which only anecdotal evidence is given, it's important to see that the author does not claim science has some kind of "superior authority," nor does she dismiss the anecdotal evidence. The author never denies that the anecdotal evidence is true: it might be true that certain people have always experienced acne after eating large amounts of chocolate. The author just provides an alternative interpretation of why that happens: eating large amounts of chocolate and experiencing acne happen together not because eating chocolate itself causes acne, but because stress causes both.

The author does not mention any well-established facts that are inconsistent with the position that eating chocolate causes acne. We cannot assume the recent scientific studies and other evidence the author points to are well-established facts. Even if they were, they aren't necessarily "inconsistent" with the claim that chocolate causes acne. It could still be true that eating chocolate causes acne, even if stress can contribute to both phenomena separately. The evidence the author provides weakens the original claim by suggesting a potential alternative explanation, but it doesn't necessarily disprove or contradict that claim.

The author does not provide any counterexamples, and certainly doesn't provide a counterexample meant to show that causes don't have to precede effects.