No one really knows yet. We have immune system issues in my family ranging from Crohn's disease (both myself and my father) to nut and egg allergies. Some of the research that's come out specific to Crohn's disease is that people who live in or immigrate to western societies are more likely to develop it. There's also a correlation between Crohn's disease and northern latitudes. There appears to be both a biological and an environment component to it, but more people are getting it now than ever, but the symptoms are very clear. You develop ulcers in your intestines, often around the ileum. There's no faking it. Severe allergies likewise can't be faked. When you see someone's face puff up, eyes swell shut, and struggle to breath, there's no denying that it's real.
Maybe it's vitamin D deficiency, maybe it's diet, microplastics, adherent-invasive E. coli, not enough pathogen exposure, some combination of these things, or none of these things. I suspect that many of these kinds of immune system issues are related but not always caused by the same triggering issue/event.