Chunks Being Weird (Not The Normal Chunk Error)

When I was exploring in a forest, I noticed a Chunk Error clipping through a mountain, so naturally, I went to hit some blocks around it to update it (along with doing F3 + A) and to my surprise, it was filled with water and about 7 squids. Im sure what happened here is that the game rendered the bugged out chunk as a regular land formation (instead of as a ravine or cave, which is not affected by sea level) and filled it with water at sea level. Not sure how, since usually it just fixes itself with a block update or the classic F3 + A...
But like I said I didnt do this manually, as I only have 2.51 hours on this world, and most of it has been spent underground in caves. (as you can tell by the dungeon loot and diamond gear)