When smelting 2 different metals, like 2 tin and 1 iron, it converts the iron to tin. (That was just an example)
Currently combining metals is not an implemented feature, so when you put different materials on the anvil at the same time, the game has to choose which of those materials to output. In order to prevent exploitation, it'll default to the cheapest ingot on the anvil. Until the system changes, it's best to just put one material's ingots on the anvil at a time. Happy Smithing!