This has been happening for awhile, but I can't point to a particular snapshot or version. I've noticed it in 1.6.x (but that was modded Minecraft) and the most recent snapshot. I was blaming mobs (spiders, etc.) until I installed a small crop farm underground that is completely isolated from hostiles and friendlies.

At Y level 34 I created a 9x9 area of farmland with a water block in the center, covered by carpet. Jack-o-lanterns surround the entire farm plot. No mobs can spawn in this area and it is protected from incursion. Occasionally, for apparently no reason whatsoever, farmland will become untilled. I am not jumping on the farmland, and untiling has happened even after extended periods of being AFK with the chunk loaded or away from the chunk entirely. Sometimes it will be just one farmland block, sometimes as many as 5, and it can occur in any location on the plot's grid and are not necessarily clustered.