Glad you're liking the game. Thanks for pointing out that bug, I'll see if I can fix it.
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.
I have finally had a chance to fix this bug (let me know if you find otherwise.)
Yeah, all the rocks use the same scoring mechanism, and initially I was a bit confused, because I definitely had logic at the top of the procedure to set the rock's score to zero if it wasn't on the board.
I spent a while thinking that somehow how it detected 'on the board' wasn't working. Finally, I realised that while I was setting the score to zero for these rocks, I wasn't actually stopping it from carrying on through the rest of the scoring routine anyway!