Is this a problem or normal
Take some pictures closer and further away to show the problem, and start a thread in the Cleaning And Restoration section of the John Bridge Tile Forum. One of the members there is a specia-list when it comes to stone care.
Rust on natural stone can mean that there is some metal in the stone. Lemon juice and baking sode may remove some mild stains. Tough stains may require acids (Oxalic) that are available in stores.