This is related only to the bigger version of the greenhouse, the one shown in the image below. Smaller greenhouses don't have this issue.

If you drop an item on top of the dirt part while holding the G key, the item will be placed properly on top of it.

If you throw an item on top of it, or anywhere inside of the greenhouse and it slides away toward the dirt part, it will go through the dirt part like there's no collision for it. This makes smaller & flatter items completely disappear and you're unable to retrieve them. Pretty much anything that isn't a large bag, or boots, or lands vertically, will be lost...