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You sure you're not just eating poorly and thinking you're eating healthy? There's a significant amount of misinformation in nutrition, on par with climate denialism.
That is almost a given. There is a lot of disagreement on what healthy food looks like, and a lack of foundational research on health outcomes of different diets long term.
Healthy food for different populations is the food that sustains health, even if that food by itself isn't universally healthy for all humans. Dairy, Gluten allergies, etc. There are many foods that some people can tolerance, but not all people can tolerate. Western diet and first nations people don't often mix well.
Even in the health research space, there is considerable, and acerbic disagreement on what is healthy vs just tolerated. For individuals its even more blurry, there are many religious, philosophical, and cultural reasons people maintain a food bias for.
A elimination diet protocol is the single best tool a individual can use to find out what is causing them problems. Get down to the very bare minimum of nutrition (meat, salt, water), stabilize for a few weeks, then reintroduce foods very slowly until they are able to identify what they cannot tolerate.
There are also plenty of reasons “healthy” foods might absolutely fuck with your health, even if you’re not eating a ridiculous amount of them. For example whole wheat is a perfectly fine food to have in your diet, unless you have celiac disease and don’t realize it yet.
Yes, allergies and rare conditions are a thing sometimes. In your own example that doesn't change the principle that whole grains are still the cornerstone of even this hypothetical person's diet - they just have to avoid gluten.