RMXP GLTICH?

When I test play my game, some tiles completely vanish and become impassable, even when set to passable. I know its not due to anything above the layer, as it is top layer, and it cant be middle layer as i havent even touched middle layer. The strangest thing is, the entire tileset is passble as i havent configured it yet. Does anyone know why i get vanishing tiles and/or how to cure them?