I've had pain in my upper left abdomen for 2 months now and had a colonoscopy. It came back clear, but they showed me pics of where it was stained, and it was brownish with little bumps due to the fiber pills that I take. They said it was nothing to worry about and wasn't the cause of my pain, so I guess there's nothing wrong with a stained colon.
Creatine doesn't stain the colon. Stimulant forms of laxatives that contain anthraquinone compounds do. I believe it's called melanosis. Also, there are some foods like rhubarb that can 'stain' the cells of the colon if enough of it is eaten (but it would have to be a heck of a lot).