Are you playing on the Wii or on the PC? If you are on the PC, could you send us the save file? I've only ever heard this happening once before and we couldn't recreate it. I'd love to track it down using the save file if possible.
As for fixing the problem, I'm afraid you will probably have to load a save from before you started digging the holes. It's non-ideal, but you shouldn't have the problem happen again.