There is a possible bug with some of the tilesets where, even when an item is alone on a tile, the little icon will appear, as if there are other things on the same tile.
This happens with MShock32Modded (yellow icon), and also with both the ChestHole and ChestHoleTileset tileset (red icon). With RetroDays20px, some items appear as they should, while others, such as a ball sat on a pool table, also have the ‘multiple items here’ issue, and subsequently show a blue box around them. With RetroDays20px, however, other items appeared as they should do, without the blue box, when they were on their own. These are the only tilesets that I have tested, so it may exist with the others too.
Sorry if this isn’t very clear, but I hope I have given enough information to find the problem, if there is one!