This is probably caused by some sort of delay in the code, like it doesn't know to call the method to break the bottom one soon enough. But when you break the top part of a two block tall plant there is a short delay before the bottom breaks and there is also two breaking sounds.
Is this still an issue in the current Minecraft Snapshot 15w47c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.