The 5D Mark II Team blog reports a problem in firmware 2.0.4 which occurs when the Canon EF 100mm f/2.8 Macro USM lens is mounted on the camera. It the user manually changes focus (rotates focus ring), the lens changes the iris/aperture “by itself”, even when the camera is in full manual mode. It does not happen in Firmware 1.1.0.
More information can be found here: Malfunction in Firmware 2.0.4
[UPDATES 4/6]: Canonrumors notes that this might be a function of Macro lenses rather than a "bug" though it's odd that in the original report there was a specific claim that the lens did not behave the same way with the previous version of the firmware.
Meanwhile, the 5D Mark II Teams post has been expanded to include notes about some third party lenses making "weird noises."