This isn't actually a bug but it might not be designed well (I can say that because it was me). It's not using 2. The slot in the forge which holds the modifier item is actually a full on storage slot that you are moving a rune into. This means that as soon as you select it, one has been moved and the count in your materials panel is one less. When you used it, another was automatically moved into the modifier slot. If you clear the slot or select something else, it will get placed back in your storage.
Edit: airowird has been around for a long time, I think they were just having some fun, no need to downvote so hard.