I can second this experience but with a twist. They admitted to the problem! I'm in San Diego and was direct to the UTC La Jolla store by an Apple support rep to pick up a replacement phone.
When I arrive I was immediately turned away because apparently they had so many people come in to replace phones they were supposedly out. After calling the support rep back and having them call that Apple Store back personally, I was directed to the store manager.
The store manager went on to say that not only were many people returning for replacements, when they were opening the replacement white box phones, 8 out of 10 were damaged in some form.
She instructed me to go home and enjoy the phone that I had until Apple could resolve the issue and they had proper replacement in stock.
I decided to take my chances and have them open one more. I apparently got lucky and found a undamaged phone. In the end, both the Apple support rep and the store manager both acknowledged this was a problem, and I think one Apple was obviously not prepared to handle.