Some people map floors or walls using tiles set in the B-E tileset, rather than from the A1-A5 tilesets. Placing one tile from the B-E tileset on another tile from the B-E tileset, would effectively replace the former.
Assuming that the floor is from the A2 ground tiles, and the wall is from the A4 wall tiles, tiles from the B-E tilesets placed on them would not replace them.
Some tilesheets downloaded from the internet come in either JPEG format, or lack transparency (ie. have a solid colour as the background). To check the transparency of your image file, you can use GIMP or any other image processing software.