Be careful of what you put on the higher layers. The walls are on the bottom layer, but if you use a blank tile that's set to passable on a higher layer, you won't see anything, but the passability will override the lower tiles and you'll be able to walk through things. If you had something on the walls and "erased" it, the best tile to use is the very top left one.
Unfortunately you can't SEE if you've put the wrong blank tile there, so I suggest you go to the middle and top layer, use that top left tile and just place it on a couple of spots that you can walk over. See if it makes a difference - if it fixes the problem you know you can go and spend the time fixing the rest.
Also putting an event marked as Through will let you walk over something, regardless of the passabilities of the tiles below.