Transparency issues. Basically if a terrain item uses a fallback sprite as an assignment in tiles mode, the transparent areas the fallback sprite doesn’t cover will basically not exist. And much like a hall-of-mirrors effect in most first-person games when you noclip and view the nothingness beyond, the “nothing” gets filled in with anything available, depending on what’s already rendered.
The same thing can occur with tiles that have transparent or partially-transparent sections, if the tile_config doesn’t assign a fully opaque tile as a background. An example is most of the window and glass wall sprites in unmodded MShock. Ever moved and saw a ghostly image of something nearby in the window? Relax, your game isn’t haunted. It’s just partial transparency combined with certain window tiles not having an opaque background assigned.