Doctors are very quick to tell you, "Eat whatever you want, until something bothers you." The fallacy here is that you may not have an immediate, obvious reaction to foods that are encouraging inflammation in your digestive tract. For most CD patients, a good rule of thumb is to avoid anything that's going to scratch up and irritate your intestines (popcorn, nuts, corn, husks, seeds, whole grains, the skins of raw or cooked fruits and tomatoes), anything that's full of caffeine (which stimulates your digestive tract to empty itself) or sugars (ditto), anything that's incredibly fibrous and hard to digest--and sometimes things that are highly acidic (tomatoes, citrus fruits) or contain milk products (if you're lactose intolerant). It's also a very good idea to avoid alcohol as much as possible, especially considering its interaction with many CD meds, and vegetables that increase flatulence (uncomfortable!).
Even if you don't feel it at the time (or afterwards), some of these things can irritate your digestive tract and make your inflammation worse.