This may be a known issue and likely is because it happens to me a lot so I assume it has to others as well, but I think I found the cause for it. Maybe it isn't. If isn't , sorry for wasting your time.
1.grab any plant with your mouse.
2. get it out of your inventory so its sprite disappears from your mouse
3. grab different item from top row
4. the item should be gone.
this works with any plant, and it can make any item disappear. I was in a world with caves if that helps anything. Doesn't work while the game is paused. Mods where on in this, but I tried the same way in a different world without mods and it still happened