Well, eggs just triggered me. I am from the "I will stop eating eggs when there are no chickens anymore" team... And sure, you're definitely right. Learning about and eliminating aspestos, for instance, was probably one of the bigger well known positive counter-example from the previous century. However, I can't think of many great counter-examples when it comes to dietary advice and the science journalism (thanks for the word) attached to it. Maybe you can poke a hole in my confimraton bias?
Now the acidity in artificially sweetened soda makes peoples' teeth bad. My dentist mother is furious about that people believe that it is only the sugar in the soda that is bad for the teeth.