Ah, I think I understand what you mean. The plain repeating tiles without any transitions or edges, right? Well, since it's meant to be tiles for RPG Maker, there was no need to include those tiles by themselves, you can get them by using the autotile correctly. You have to do some copy and paste or use it as 16x16 tiles to get them working in non-RM use. The sample maps were created using the artwork included with the pack, so if that's how you got them I don't mind at all.
Thanks for the quick reply. It makes sense that you'd not worry about them if your tool takes care of it for you. I am using TilEd maps loaded into Java/LibGDX, so needed the tiles in my map. The files I cut from your samples will work fine for my project.