The problem is that in IMAP the concept of labels doesn't exist. Thus they are implemented using folders, which is a concept in IMAP. But that issue is, a message is then in multiple folders (to reflect that it has multiple labels), but in the way this happens in IMAP, they are different messages, even if the content is the same. And thus I can imagine, automated programs, not aware of this, may for example see 2 invoices (because the email has 2 labels) rather than 1.