The reason why you get food intolerances and start reacting to foods is because you have an imbalance inside your intestines. It can create something called 'Leaky Gut'. What that is - inflammation of your intestinal lining. Instead of having tight junctions together, you get gaps between those intestinal cells.
Once you have gaps, whatever food you eat, it passes through the gaps. Then, it goes through into the blood undigested and your immune system perceives this food that you've eaten as an intruder - it thinks it's a virus trying to attack the body.
So your immune system creates antibodies to that food you just have eaten and every time you eat that food, it sparks an immune response.
Your immune system creates inflammation inside your body that is why you start reacting to foods and have food intolerances.