I gotcha now. The earlier statement had me thinking you paid two separate charges and they should just refund the one. You just meant that you got it itemized out, so you knew how much each thing cost. But they still just did one charge for the total on your card. Got it.
My experience with credit card companies has generally been very good in getting bad charges taken off. Hopefully, you will have similarly good luck! Heck, I hope you are disputing the entire charge. Dispute part because it was not discussed and the other part because it was discussed and they told you it was be a no-charge warranty repair. You only gave them your credit card info and approved a charge for the return shipping.