Nessa hit it on the head. Scar tissue is one of the biggest reasons for pain. Even when I have been in remission I have had the occasional pain because of scar tissue. When waste forms into stool as it moves down the intestinal tract it is "rubbing" against the scar tissue and will at times cause pain. We can't see inside our intestines so we don't know the extent of the scar tissue. It can be anywhere even if you have never been DX in other areas.
So there will be times when you swear your CD is flared up and it just turns out to be scar tissue causing problems. You really need to be able to "learn" what your body is doing and than you can decide the best course of action to take whether it be call your DR or just take it easy with your diet for a little bit.