When my brother took his iPhone 6 with cracked screen back to Apple store, they asked $109 to fix it. After he agrees to that, they told him the glass repair machine was broken, so they gave him a brand new phone instead.

When you took your original iPhone 6 to Apple store, did you tell them everything or they found out themselves? If they don't have it in the system, you could just try another apple store. Just tell them you crack the screen and want to repair it. It is only $109 and you may get a new phone instead.