Eggs are the usual example. US regulations require eggs to washed, removing a protective coating, which is why Americans refrigerate eggs. Many other developed nations forbid washing eggs with solutions that would remove the same protective coating, so eggs are frequently not refrigerated there because they don’t really need to be. The motivation in the US was avoiding salmonella, but other places have avoided that by improving cleanliness practices of the farms rather than washing their eggs.
Kind of different, but recent requirements to label foods containing sesame as an allergen led to more foods having sesame intentionally added, since it’s cheaper to add it intentionally and then label it than to prove the production facility and ingredients are 100% sesame free. It’s not removing some natural defense from a food, but that’s a regulation intended to help people with allergens stay safer which inadvertently decreased their options (and maybe made it more likely they’d buy something containing sesame by mistake if it was a product they’d been safe with before but had recently added sesame).
So I very much agree with you that the food regulations of the FDA and similar institutions in other countries are largely a blessing and huge boon to human welfare. It’s great to be confident my bread isn’t 50% sawdust and there probably isn’t melamine in my milk and stuff. But like any big regulatory environment mistakes have been made, and also sometimes regulations that made sense at one time outlive their usefulness.