When harvesting wheat and betroots with a Fortune enchanted tool, only the drop rate of the (betroot-) seeds get effected and not that of the actual item (wheat/betroot).
In the image below you can see the drop rates of 20 fully grown crops each type with Fortune III on top and without at the bottom.
I think this is not a bug since the seeds are the only things without fortune you might get multiple of on wheat and beetroot crops. I think, instead, this is Works As Intended.