All the blocks in a square area were deleted down to bedrock

Put the summary of the bug you're having here
I walked over to a wall I built and there was a large square hole in the ground going all the way down to the void
What I expected to happen was...:
I expected to see the cobblestone wall

What actually happened was...:
Part of the wall was intact, but the rest was gone. Instead, there was a large hole in the ground. I switched the gamemode to creative and went inside and I fell very slowly. The edges of the pit were not lit, I could not place blocks inside the pit, and water would not flow into it. Also, the sky darkened when I went inside it.

Steps to Reproduce:
I am not exactly sure how it happened, I walked over and it was there. I did not see it happen. This has happened to me once before, though, in 1.6.4 in the Nether.
1. create a world and switch it to survival mode
2. go do whatever. It might happen, I am not sure how often or how long it takes