I am having problems adjusting the aperture when using manual. i can move the shutter speed and iso but not the aperture.What i do is flick to AV change aperture and then flick back to manual, must be a better way.
I have aperture change on top dial and iso on back dial. My MKIII has the same problemYou probably need to check the configuration of the buttons & dials as you can change which dial does what. Personally I have aperture on the top dial and shutter speed on the rear dial.
I believe that you can tweak the config so in manual you may have an accidentally weird setup.
Check custom function IV - 5 "Tv/Av setting for manual exposure"