Please make screenshots of your tileset definitions, and mark the tiles you have used on them.
There are several ways how this could have happened, either because of a wrong tileset definition or because you used the wrong tile - all Autotiles have special functions, and if you use a tile in a way it's not intended to be used, then the walkability can be broken.
Addendum:
I just checked the tilesets, and the tile you've used for the wall is NOT a wall-tile, it's a topwall-tile, and those have special passability and are intended to be walkable under special circumstances.
Go to the link in my signature, scroll down to the tips (third post) and then read tip 7 about A4-walls and the simulated two-layer-dungeon possible with them.