Pistons are destroying breakable blocks when they pass through them.  For example, if I have a sticky piston in the floor set to push up when I press a button and I have a sand block attached to the piston with cactus growing on top, if I let it grow to 3 high, I only get 2 blocks back when the piston is activated.

I find the same thing happening to watermelons, pumpkins, cactus, bamboo, sugar cane and cocoa beans.  All the foods that are usually dealt with farms.  Anything that consists of one block is destroyed.  Anything that produces more produces one less item.