Major Chunk Errors

After generating a new Superflat world, having previously generated one under the same name but forgetting to set the "Superflat" option, lots of Chunk errors started appearing, some of the world seemed to be superflat and some seemed to be normal. An NPC village was located near spawn, some of the village spawned underwater, some near bedrock (Superflat setting was the default 3 Blocks to Bedrock), some was high up on stone/dirt pillars. Also, there were air pockets in the oceans, and after exploring the world a little more I have found out that the issue seems to be spread over the whole world. I have attached lots of screenshots and also the save file, as I do not know how I could recreate this. Also, some of the lava flowed over the edge of the chunks and some didn't. I know that chunk errors are not always bugs, but something this big was something to report.