I have a giant folder hierarchy in my gmail, so I assure you this can work. In your case it sounds like you're taking a message with the "Inbox" label and addi

I have a giant folder hierarchy in my gmail, so I assure you this can work. In your case it sounds like you're taking a message with the "Inbox" label and adding the "some/folder" label, which will indeed still show it in both places. If you move the message, which removes "Inbox" and adds "some/folder" it will no longer show up in the Inbox.