I started to work on building a huge lighthouse yesterday in Alpha. Once I used up all of the cobblestone I had in my inventory, I went to mine more. After I returned to my lighthouse with more cobblestone I saw that about a quarter of the circular wall was missing. It didn't look like creepers had gotten it or anything. It was cut perfectly from the rest of the wall. I just dismissed it as a small, random glitch and just rebuilt that section.
I logged on again today to work on my lighthouse and, after having to mine more cobblestone, I returned to find that another quarter of the wall was missing again. It wasn't in the same place as the last hole though.
Is there any explanation for this or is it just some random glitch? Is it possible that that save file is somehow corrupt?