Have just had a colonoscopy and they found some aphthous ulcers in my bowel. what are they?

Not aphthous ulcers: Aphthous ulcers are generally painful ulcers that occur in the mouth. Typically called 'canker sore', they are recurrent. Since aphthous means ulcer (latin, it's all in the latin), therefore it is a redundant term, and more accurate is the diagnosis of 'aphthous stomatitis'. Among the many associations with other problems, one is a colon disorder known as crohn's; but the ulcer is in the mouth.

Colon aphthous ulcer: Sorry for confusion, but gastroenterologists commonly use the term "aphthous ulcers" to describe small ulcerations in the colon & small intestine. When terminology is applied precisely, the ulcers are associated with inflammatory bowel disease. Descriptively, but less precise, ulcers of similar appearance are seen in the lower GI tract with use of aspirin, with lymphoid hyperplasia, herpes, others.