Hello Enzo, sorry to hear you're having trouble.
You're correct that the purchase should also incorporate the balance of the order. However, as it did not seem to be used for your purchase you may want to try requesting a refund then try again. You can request a refund via https://xbox.com/refund.
But I would also recommend starting an online chat with support via https://support.xbox.com and click on Contact Us for more help. They should be able to look into the payment information to check on what happened.