The customer service people you speak to on the phone or on-line generally seem to be reasonable, and certainly better than a lot of on-line stores. Still, this kind of thing happening in the first place is also poor customer service. Other dumb stuff is also far too common at Amazon in my experience.
They frequently seem to ship fragile items in nothing but a standard cardboard box with negligible padding so they're smashed to pieces by the time they arrive.
Recently I've seen several "new" and yet obviously not new items like books with bent spines or DVDs with fingerprints all over them.
They sometimes give wildy optimistic estimates of delivery dates particularly around holiday seasons when everyone is buying presents. Worse, they seem to have multi-week standard processes for deciding when something has really gone missing before they will try shipping another one, which is no use at all if say you're ordering Christmas presents in December.
Even if they are happy for a customer to return something for a refund, it's still a hassle for that customer to ship it back or arrange the collection every time something goes wrong. Even if they'll refund an order they found they couldn't ship when they said, the customer has still potentially lost several days in the process and might be too late to order it from somewhere else instead.
I suspect in some ways Amazon have been victims of their own success. I wonder whether anyone has ever tried to implement such personalised logistics at the scale Amazon does before, and given how often ordering from them does lead to a better experience than we used to have with bricks and mortar stores, I hesitate to criticise too much over things going wrong. There is definitely plenty of room for improvement in the customer service department, though, and at least part of it appears to be due to deliberate policies and perhaps cutting a few corners too many to try to shave off every last penny in running costs.