What happened is that when Apple did not receive the trade-in, they added a charge to the card for the amount of the credit.
Anyway, the important point you're missing is that if Apple was dealing with a Chase card, Apple would not be out any money, because Chase pays Apple for any charges to the card. You're conceiving of a scenario where Apple doesn't get all of its money, and that's simply not the case with a third-party credit card.
Now if Apple and Goldman Sachs operated in the same manner, then Apple would also get all of the money it was owed, from Goldman Sachs, and then it would be up to Goldman Sachs to get payment from Dustin, which is no concern of Apple's. But apparently Apple and Goldman Sachs have a different kind of relationship with the Apple Card.
It appears that Apple is using its iCloud leverage to force the card holder to pay Goldman Sachs. Apple would have no such leverage to force the card holder to pay Chase, nor would Apple have any desire to use such leverage for Chase, because Apple is not "in bed", so to speak, with Chase.