I would guess food sensitivities. They are more common in Crohn's than the general population. For some idea of what foods etc can cause a reaction, have a look at this abstract: Immune sensitization to food, yeast and bacteria in Crohn's disease.
This is only an abstract, but you can get an idea of the kind of thing that causes problems. It can be almost anything from the normal diet. Fortunately, if you can avoid the triggers for a period of time - usually a few weeks and up to a couple of months, the reaction fades (for foods). You have to learn how to tell when something causes problems, but that is hard when there are several common food classes (wheat, dairy, corn and so on) that you react to. If you are always reacting to something, you can't tell which something caused the reaction. The approach that works is to eliminate everything but a very few foods that are usually safe and then slowly add foods back into your diet. That is the approach that the SCD plan takes. It works for a number of people, but it takes time and effort to educate yourself about
the common sources of trouble. For some idea of just how this works, have a look at: http://pecanbread.com/p/legal_illegal_a-c.htm
There are other pages that detail the starting diet which is really difficult, but doable if you're serious enough about
working on this problem. The diet reflects the experience of many people and the reasons for some restrictions are probably not fully understood, but they work for many people, but not everyone. For instance, one report cited problems caused by microparticles in food, including things like flow agents added to spices or dirt on fruit and vegetable skins.