On some replacement screens, there is not always the Chip for the touch ID to clip into so people just leave it hanging. The clip part is connected to the digitizer of the display and new third party displays can't always replicate Apple with this.
The only way you can get this is by getting a really good display or going directly to Apple.
This was differant than the 5S's just because they connected to the actual body of the phone and not the display itslef. So you have to be careful when getting iPhone 6 Screens replaced.
I would go back and asked if it can be fixed or if the display just doesnt have the capability to do touch ID (I would be asking for my money back)
Ta!