Actually, I think I know what the problem was. I put over 3 checks just to confirm that a tile is ocupied because sometimes the game just won't recognize it for some reason. What happens (or what I think was happening, was that one of those checks was if one plant was over another object, which was the tiles. However, what I didn't realize as I made the tiles invisible (so the background tiles would seem as the actual tiles) was that actually, the plants were created on a lower layer than the tiles, thus a plant would never be above said tile, which could cause an error. If this doesn't solve it then I don't know what it could be. Hopefully the new version won't have any bugs.
Edit: I uploaded it and it seems it has been fixed. At least the bug I found before seems fixed, and luckily, the bug you found is so.