Every once in a while, when I log off and relog, sometimes blocks respawn in places I have already mined out(Sometimes also trapping me in said blocks), and if there are any other blocks there(i.e. Chests, Redstone components, etc, they will be overwritten as blocks of stone, dirt, ore, etc(You lose the items completely)
Edit: Upon flying around in ./gamemode 3(spectator mode) I found the blocks that were overwritten by the stone, dirt, etc. moved to a different part of the map nearby.
Edit 2: I have included photos of my wheat farm that dissappeared, and find below in comments the requested game log.