They probably didn't know.
I realized the last time when I added my email address to calibre, it started auto sending it to my @kindle.com account every time it updated with new updates. What I think could have happened is that, instead of sending the one copy that you thought you had sent, calibre automatically sent the rest of them too. and Amazon just deducted money from you for the sending mail service. Surely, they didn't charge you for the subscription price. Just for the mailing of the 3 papers that got auto-calibre delivered.