I just had the same thing happen with an iPad air. Didn't realize you could take it to the store (we even did store pick up of the new iPad mini and MacBook air we purchased! live and learn!) sent in a perfect iPad air (this thing was barely used as my husband hated the size what he wanted it for and was in a case on his desk!). I did forget to take the screen protector off. I was shocked when I got the email. I called and the CS rep looked at the photos and said she didn't see anything wrong and submitted to the warehouse to take off the screen protector and re-evaluate. within a couple hours I had an email saying investigation was complete and I'm getting my refund to my original payment.
Next time I'll take it to the store as advised by her and this thread!