Organic particularly means "no roundup". Non-organic crops tend to be round-up resistant strains. If the seed engineers for said strains weren't being careful, they could have affected other aspects of the seed's physiology while selecting for round-up resistance.
One concrete example is how certain modern strains of apple seeds have weaker dormancy, causing imbibing and radicand emergence to occur prematurely, usually before the apple is even eaten. Such changes are an unintended consequence of human selection for size. It's possible that the tinkering required to increase plant vigor in the presence of non-organic pesticides has a greater adverse effect on mineral content. Though there are lots of other variables to consider as well such as soils, fertilizers, storage and transportation, the positioning of plants, whether they are able to share nutrients.
One concrete example is how certain modern strains of apple seeds have weaker dormancy, causing imbibing and radicand emergence to occur prematurely, usually before the apple is even eaten. Such changes are an unintended consequence of human selection for size. It's possible that the tinkering required to increase plant vigor in the presence of non-organic pesticides has a greater adverse effect on mineral content. Though there are lots of other variables to consider as well such as soils, fertilizers, storage and transportation, the positioning of plants, whether they are able to share nutrients.