Let's say you're using C-AF to track a bird, and the bird suddenly goes stationary. Well, sometimes, the quickets thing to do is using manual focus to nail the bird, instead of having to change from all AF points to single point.
That's me, anyhow.
I also remember reading of a guy who used an E-3 and a 50-200 SWD to shoot some American Football. Well, he tracked and he tracked during the past time, but then out of nowhere some people let out a bunch of balloons, and the AF just wouldn't understand that this VERY big punch of bright colored things weren't the motive. So he took his finger of the AEL/AFL button and focused manually, and nailed it.