In inflammatory bowel disease (IBD), ulcers form on the insides of the intestine. In ulcerative colitis, the ulcers are found in the inner mucus lining of the intestine. In Crohn's disease, the inflammation goes deeper, and ulcers can permeate into all the layers of the bowel wall.
People with IBD also sometimes develop shallow ulcers in the mouth, known as canker sores, or medically as (aphthous stomatitis), which is an extra-intestinal condition. Canker sores are annoying, but not usually serious. They're common among the general population, too.