In 2010: Odyssey Two, the Russian spacecraft Cosmonaut Alexei Leonov finds the derelict spacecraft Discovery rotating around its pitch axis (end-over-end). In the book, I believe this is explained as angular momentum which has transferred over the years from the centrifuge room to the rest of the spaceship. I don't think they bother to explain it in the film.
I'm not sure if there's a canonical layout of the interior of the Discovery, but all of the fan art on the Internet places the centrifuge at the back of the globe structure, with the centrifuge's central axis in line with the ship's long axis. And in fact, there's kind of a "cap" on the back of the globe that might help accomodate the centrifuge:
But if the centrifuge's axis is along the Discovery's roll axis, then transferring that momentum to the rest of the ship would cause it to spin along its roll axis, not its pitch axis. So why is it found to be spinning the way it is?