I think the question is about the cultural taxonomy, not the scientific one. For instance, culturally, tomatoes are often a vegetable in the United States, but botanically they're a berry and therefore a fruit. A culture could either treat fungus as in the "plant" category or not in the "plant" category and both would be culturally reasonable.
(It's also an error to claim that it's "wrong" to call a tomato a vegetable. Words have different meanings, and you're in for a lifetime of frustration if you go around insisting that cultures are only permitted to use all words in exactly the way that scientists use them.)
In context, it was clearly saying that a tomato is a fruit/berry in a biological context, but a vegetable in a culinary one. That doesn't mean that those words don't also have different meanings in other contexts.
Just as coffee "beans" are actually seeds. This information is of no use to the vast majority of people unless one finds it enjoyable to be pedantic, but it is a neat bit of trivia all the same.