Filled blocks not being saved

When I used the command /fill to fill an area of 900+ dirt blocks with air, after exiting to title and going back in the world, first I found that two random large chunks of dirt had appeared in an empty area I had created, along with (very strangely) a dirt bridge I had made right after I had cleared the area before and destroyed long ago, and a few random blocks from fixing structures that I had also destroyed before.
Then, I cleared it again (twice for one dirt chunk) and I managed to stop the dirt bridge and one large chunk (except for a few random blocks left behind) from reappearing when I relogged. After this, I set a command block with the fill command to get rid of the other large chunk because I was getting sick of typing the whole /fill command. What I found when I saved to title and went back again was the command block was there, and the dirt chunk was, so it didn't remember it being filled with air again. I won't be surprised if I clear and relog a few more times and it will disappear, save a few blocks but I don't want to have to clear another bunch of chunks that might appear if I do.