I'm assuming you've set the bitmask mode to 3x3 minimal.
You don't seem to have all the required bitmaps set. 3x3 minimal requires 48 tiles, because that's how many bit combinations are required to cover all the possible tile arrangements.
Here's a link to a picture with all the required bitmasks defined:
As you can see, you're missing some, plus you have duplicates defined in the upper left portion. Autotile does not care (or know) what the tiles look like, it just needs all the correct bitmasks so it knows which one to choose based on the tile's neighbors.