Because of the map changes these herbs cannot be reached anymore. They float in the air in impassable terrain, and because of that they make it unable to be removed and have new things planted. This was also the case in the badlands in the area around the fish barrel, and may still be the case there where the plants were hidden inside of the cliff itself. Those were on ground level though so they can't/couldn't be seen when the map was changed and the area covered up yet still take up planting spots.
(http://i.imgur.com/gMm3TkC.jpg)
Should be fixed.