Why won't apple replace my iphone 6 screen?

This week I went to the Oakbrook, IL Apple to get the screen on my iPhone 6 replaced after someone cracked it a few days prior. The Genius bar member was helpful and said it was a routine process, takes my phone into the back and says it'll be about 40 mins. Some time later, my phone comes back out, I'm ready pay the $109 and be done and I notice that my screen wasn't fixed. The guy tells me that they found signs of the screen being from a 3rd party. This was ridiculous because I have never needed to replace my screen and had I ever needed to, I would've gone to the Apple store. I pre-ordered the phone direct from Apple in Sept. of 2014 and it has been the same phone since the day I received it. I called to complain and I spoke with a very helpful gentleman that spent over an hour trying to get it fixed for me, even offered to waive the fee but the Oakbrook store technicians were final on their report and refused to look at it again. How ridiculous is it that Apple uses "non-Apple" parts on their products!