This really bugs me. It's a difference between how the game and the editor display graphics.
In the game, whenever you have two transparent tiles or objects on top of eachother, they add in effect (meaning if you have two shadows on top of eachother, they turn darker, and if you have two glowing things on top of eachother, they get brighter).
In the Editor, two transparent tiles add in effect
only if they are different. This means that if you place the same transparent tile on the same square in two different layers, it will look like there's only one tile there.
Not only is the editor's display behavior unintuitive, but it also means that a level might look different in the game than it does in the editor. This is demonstrated in the attached image.
Is this intentional? Seems odd to me...
This puzzled me a lot a while ago when I was using the Lasers tileset in my level. The lasers aren't particularly bright (not against a green background, at least), so I always had to double them up, and it bugged me that I always had to pick different lasers in order for them to look brighter. Just today I tried putting orange on orange and realized it was still bright
in the game even though it wasn't in the editor.