These plant foods contain anti-nutrients (for instance, phytic acid), which prevent proper digestion. In Chris Kresser's article: Another reason you shouldn’t go nuts on nuts, you can find more details about the phytic acid content of different foods. From an evolutionary point of view this makes sense: plants have no other protection from "predators" than the storage of toxins in the husk and, to a lesser extent, in the grain itself. The purpose of the grain is to avoid digestion by the animal's digestive juices, and end up intact a few miles away from the mother plant. This is the way plants propagate.
Fruits function pretty much the same way, the difference is that their seeds (usually indigestible) are coated with a delicious sweet layer. This attracts birds and other predators, thus increasing the plant's chances for propagation.
Traditional societies knew how to prepare grains to remove toxins. They also knew that raw grains and nuts were not digestible. These methods of preparation include:
- heating (cooking)
If we skip some of the steps, we end up with the conventional white bread so commonly consumed. Our body is not used to process this new food. We are especially not used to the amounts of carbohydrates our civilized diet is based on.
I would like to emphasize again that all deficiency diseases appeared in populations where grain consumption was the highest. Interestingly, populations with a diet high in animal fat and meat, did not display symptoms of deficiency diseases, including scurvy (vitamin C deficiency). For more: Vitamin and Mineral Deficiencies.