You sure they knew what you were talking about and didn't just give you credit for a phone they thought you owned outright? Why would they give you anything back on your card?
I only ask this because a few years ago, in Connecticut, i tried this exact thing after I had issues the year prior with someone stealing my trade in at the FedEx depot in Norwich. I had to deal with Apple for weeks after that until they finally closed the case and sided with me.
Trying to avoid that mess again, the following year i went to an Apple Store hoping to just hand in my trade in after i had already received the new phone from UPS. However, nobody had any idea what i was talking about! They had actually never even heard of the iPhone Upgrade Program at that time. Not even the store manager who they got to come out to chat with me. They tried to give me a trade in value on the phone, not understanding what the iPhone Upgrade Program was or how it worked, and that it should just cancel the rest of the loan. It was completely bizarre. So i've never tried it again.
I'd be very happy to hear that they actually do this now, though.