Hey Awesomeal15,
Usually putting things on the anvil works well but rarely you'll get an issue with the anvil not registering the ingots. I'll look into adding a feature that will let players know if the game registered 1,2 or 3 ingots. So if that happens, you just need to take them off and place them back on again to make sure everything is registering.
Thanx for the bug report.