Interesting you say this, I get vicious migraines from nearly all apples now, although it's less frequent during summer months so maybe what comes from the US is different. This didn't happen when I was young so I suspect they are either being treated with something different, were GMO or there is something else new I don't know about. I'll have it in apple pie around the holidays and brace myself for the migraines but otherwise avoid them.
It's very common to simply develop food intolerances/allergies as you get older. It doesn't mean there is anything different about the foods. It's just your body not liking it anymore.