If an item drop falls on a plant you can't harvest yet, you cannot pick up the item.
I had a drop of gunpowder fall at the same spot as a plant that requires a lvl 100 scythe to harvest. When I try to pick up the item, it only shows the red harvest icon. I am not far enough into the game to have a lvl 100 scythe.
Just hold E to collect every drop in a radius.