I'm having the exact same problem, and I have a theory on why it's happening.
Apple has always been aggressive in shutting down unnecessary hardware and software services when our phones are in screen off/sleep mode. Because the new Touch ID is so fast, the phone is unlocked and at the home screen faster than these hardware and software services can all turn back on.
I think this will get fixed quickly, but I also hope Apple adds an option to have a Touch ID delay of my choosing, just for the lock screen. As of now, it's impossible to use the double click home to Apple wallet feature. Really surprised Apple has a feature that is basically impossible to use. Very un-apple like, in my experience.