Ouch! Data corruption! I've had it happen to me, and I've yet to find a way to fix files like that.
It's happened to me a time or two when I've had a backup SD card and main CF card in my 5DIII, and I've checked both files, to find the corruption, which suggested to me that, in that case at least, it happened in-camera. Could also be a problem with a card, maybe make sure you reformat the cards every time you swap.