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I was stuck between 2 answers, both of which sounded really correct to me (well actually, only one of them really did and the other one just didn't sound wrong at all but had these words that were contained in the stimulus so I got tricked into picking it which ended up being wrong). So the right answer is B, which sounds fine to me and I'm not sure why I didn't choose it, but can someone explain exactly why E would be a wrong answer here?

Firstly, (E) doesn't provide any counterexamples. A counterexample in this case would be a person who eats a lot of chocolate and never gets acne. The studies cited by the stimulus reveal a 3rd factor that causes both stress and chocolate eating, but this is not a counterexample.

Also, the evidence given does not destroy the assumption that causes always precede their effects. In fact, they actually support this assumption by showing that stress and hormonal changes (the cause) PRECEDE the effects, which are increased chocolate consumption and acne.