seems this bug has now re-occured. When a plant is harvested from the plots it will seem at random that a seed will stay behind making the plot totally unable to be reacted with and needs to be deconstructed and then remade to be used.
I don't know if this was intended or not, but through at least the excellent smelter, the coal and sulphur ore can be collected and converted into ingot. But now I have coal and sulphur ingots with which I don't know what to do with.