It appears the agricultural tower doesn't properly account for the maximum possible drop when determining if there is enough space in the inventory, it only checks if there is enough space for the average drop I think. This means there are occasionally gold seeds or wood left on the ground that block re-planting. The items on the ground do get a deconstruction order, but that's not automatable until unlocking a proper bot network.
This is most likely a vanilla bug, but none of the grow-able vanilla plants have randomized drops so it doesn't show up there.