During the time I posted this and now I finally have some answers. First, during the posting period phones suffered a so called error 53 which basically was an error that when you removed the home button flex from the phone, the phone would stop working. Apple apologized for this and removed this 'feature', but phones in ios 10 and late ios 9 really had a problem when you removed them from the motherboard.
I later also discovered that iPhone 6 touch ID flex cables are very fragile and tend to make a very small crack in the location where it twists. So if you are not careful enough or you bend it around a few times it will get damaged! Look very careful if yours doesn't have a small crack in the corner. It's hard to notice sometimes. The home button will still work but the Touch ID will get disabled because of this and there will be no solution for it. I am very careful now when removing the touch ID on this location. I sometimes remove the metal back plate with the home button still attached to the flex cable. This seems to work out for me.
I hope you have learned something because of this!