TidBITS:

I haven’t been able to determine why it’s happening, or if there’s anything to be done about it, and it’s certainly only a minor irritation. I’m technically proficient and relaxed about errors that don’t cause data loss, but I am concerned that inexplicable behavior like this could start to undermine an inexperienced user’s trust in iOS as a predictable, reliable system — Touch ID is in essence lying to the user through this error message. Technically there’s no real damage here, but psychologically, it’s a bad thing — it’s important for interfaces to communicate clearly, accurately, and reliably to build user trust.

I’ve been dealing with the same (minor) issues as Adam has for just as long. It seems to be very common. There’s no real concern (these issues aren’t deal breakers) but they certainly are annoying and frustrating when they occur for no apparent reason and have no apparent solution.