Anytime you have an enchant on anything over efficiency 3, and you mine quickly, it will seem as if you broke blocks that respawn once you reload the chunk. Sometimes this causes you to suffocate instantly and others it registers after. Example: mine in the nether with an efficiency 4 pick axe, clear a decent sized area, walk out of the nether, back in, and it will regenerate a majority of blocks you had already broken. Hope this helps. I have videos of these issues if needed. Its been happening for at least the 4 updates as well. Thanks!