When you think of the digestive tract, a very specific part of the body is pictured - and it usually is not the mouth. However, the mouth is part of the digestive tract, and Crohn's disease is capable of affecting absolutely any aspect of the digestive tract. As a result, mouth sores, cracks, lesions, swelling, redness, and more can occur at any time.
You might expect that because everything on the digestive tract is connected, when one area flares up, so will the others. But this is not the case for oral flares. So, when you are having intestinal flares, that is not necessarily the time that you will have to expect sores or lesions. Conversely, just because you are safe from intestinal flares at the moment does not mean mouth sores will not appear. This can be frustrating because for many it feels as if you can never have everything under control at once, and that something is always plaguing you, even when one thing is temporarily cured - like "one step forward, two steps back."
Sometimes, especially for those who are particularly prone to mouth ulcers (often having Behçet's disease), eye inflammation and digestive ulcers can also occur.