I too have run into that situation also from time to time. The best one was a little garden wagon from Northern Tool at the time sold for $149.99 and was rated at 1200lbs. and the shipping weight was 63lbs.
So the first wagon that showed up, the box was beat all to hell and it had missing hardware. So I called and they sent out a second wagon and when I asked about returning the first one, they said just keep it for parts! Oh ok, that sounded good to me. Then after putting the second wagon together, I noticed that the metal sides did not fit together properly. The side panels tilted inward two inches when put together and didn't make a perfect rectangular wagon box. So I called back and explained that situation to the same person I had just chatted with the day before. He said just keep it and I will send you out another one no cost!
So unfortunately the third wagon had the same issue as the second, the side panels also tilted inward. The problem being the two end panels were built too short and when latched to the sides it made them tilt inward.
So after all that and with two free wagons for parts, I just left it at that and decide to live with the sides tilted in. My guess is that it is much easier for them and cheaper to just send out another one VS having to deal with the expense of the return and an unhappy customer in the end! I am sure if it was a high dollar item, that would not happen.