I think some of these touch id buttons are defective. I had a launch day iphone, and the touch id never work well. The finger sensor seemed to get worse over time. Tried all the tricks and suggestions, but it never was reliable, only worked successfully about 30-40 % of the time. I had hoped the software updates would correct the problem, but no dice.
I took it in for a look, and i was told that i must be software corruption, and to reinstall the OS and to NOT restore from an icloud backup, which I did. Nothing changed, so I took it back. The Genius was great and said that it must be a hardware issue with the phone, and he replaced the phone. The new phone is successful in recognizing my thumbprint at least 95% of the time, which is amazing.
So for those with similar issues, it would probably be a good idea to take it in for a look.