I know we know little about nutrition compared to what there is to know, but a recent article in New Scientist talked about efforts to identify and quantify some of the thousands of undocumented chemicals in what we eat. They describe a database building effort that lists 70,000 nutritional compounds in some foods, more than 400 times what the USDA database analyzes. Example: USDA lists 67 compounds in raw garlic, FooDB has 2306.
Scientists are only beginning to assess what happens to some of these chemicals when we eat them and what effects result. The article suggests that this is why so many of our statements about the benefits of a particular food don't end up being reliable or explicable; there are things going on with chemicals we don't presently pay attention to.