People often think that "science says tomatoes are actually fruits." They usually base this off something they heard in science class in school about how the ripened ovary of a seed-bearing plant is "the fruit" of the plant. They might have forgotten the specifics because you don't have to care about botanical definitions after you graduate high school, but they just remember "science said the tomato is a fruit". This belief is why this site's URL is "https://fruitorvegetable.science"
This misunderstanding is basically correct for the botanical term "fruit", as tomatoes are the fruit of the tomato plant. But it's not some universal fact that "science" says.
The only things that science really says are things that are shown via well-designed, repeatable tests. You can test how hot something burns or what effects a drug has or what a formula equates to or how people react to different things, but botany does not govern culinary terms. Scientists agree on different terms for different things at their discretion to make their research easier, but that is not science saying that, nor intended to be applied outside the botanical context.
When people say "a leaf", they are referring to the actual, botanical meaning of a leaf. It's the same for "stem" and "root" and "seed". You probably should care about the botanical definition there to communicate clearly. But other terms like "fruit" and "vegetable" and "nut" are not used in the botanical sense. Those are typically used as culinary terms, so their meanings are based on people's ordinary usages of them as food groups.
As an aside, semantics is also a field of science. If you conducted a semantical study of what people considered fruits and vegetables, you would get a true scientific representation of their categorizations. In fact, I have found a psychological study which identified features of fruits and vegetables which people use to differentiate them and another study which used those features to accurately categorize novel fruits and vegetables. If you are interested in scientifically differentiating fruits and vegetables, these are the areas you should be studying, not botany.