Thanks!
Additional information if it helps: the bug also happens for medium rocks and low rocks. I don't know if maybe the rock is recorded internally as being present but offscreen instead of being absent? It might be worth checking every item type and seeing if it gives its corresponding nothing-nearby-for-bonuses points; I've not been double-checking small-rock points and I don't think I've had a leftover lantern or shrubbery in the time since I noticed the bug.
Edit: Was able to confirm today (2020-09-27) that unplayed small rocks count for 1 point, which tracks.