When the investigators talk about "layers" they are talking about combining different images into one. For a simple example when I sign an image I can sign anywhere on the image, then move the text around until it is where I want it.The text exists in a separate moveable layer until I "merge" or "flatten" the image.
The B.C. forgers were working with different software than is used for photographs but the principles and techniques are related. They did not expect close scrutiny and expert analysis and the careless flaws and errors show.
Or purposely left that way. There are some that believe the forger was pointing to Alvin as the director of the forgery with X and smiley face.