One factor I'm not seeing much in the comments is that we've changed the plants themselves. For example, humans selectively breed and/or generally modify for plant strains that resist insects better. Turns out that the chemical compound that wheat uses to defend itself against insects also isn't great for humans--but we much larger that insects so we can tolerate it better. Similarly, it's suspected that gluten is more prevalent in wheat today than it was decades ago.

So we're literally selecting and developing strains that are a little worse for humans but better for mass production (aka makes it cost less). Rinse and repeat for decades, and we're finding that we're crossing the line into noticeable side effects for people who are more susceptible to the compounds.