When you break a crop it seems to have a chance or set a percentage on a dirt block to break it. If you continue it without attempting to break another block, it will in a small amount of time fully destroy that dirt block, if you're standing on it, it will deem it as an glitch or something and replace the block the next tick, but will destroy any other dirt block. 

Destroying a different crop without attempting to break different dirt block or any other block will have the partly destroyed dirt block at it's current state.

This will happen with bonemeal in your main hand and plantable crops in your off hand, and with only using your primary hand. I've included the main and off hand scenario in the video attached.