I see your tileset contains tiles with no visible pixels in them. They are *not* blank tiles, and you should not use them to erase things. The only truly blank tile is the one at the top left of the tileset (next to the autotiles).
Check each layer for use of those transparent tiles. I suggest you flood fill everything that's supposedly blank with some (visible) junk tile and then flood fill them all with the actual blank tile.
This is why the tilesets in Essentials draw a [X] in all unused tiles - so that you don't try to use them to erase anything, because that's not how it works.