No, no - I understand that you can think this, and that they claim it, but from a UI angle, it's wrong. I hate the implementation of labels.
They don't actually disappear when I click on inbox. When I want my inbox, I want just that folder - all filtered content goes elsewhere and disappears until I want it. That's not GMail's way.
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.
They don't actually disappear when I click on inbox. When I want my inbox, I want just that folder - all filtered content goes elsewhere and disappears until I want it. That's not GMail's way.