First off, it doesn't record your fingerprint, it takes measurements of you finger which is also somewhat unique to each individual. Back when tickets didn't expire if there was a lot of time between visits and you lost or gained weight, it had trouble reading it properly. That said, however, that is no longer the case because all tickets (other then AP) are length of the trip. The next time you go they will remeasure your print when you first use the ticket. They don't keep things on file.
It has been said that a lot of the problem comes from either not remembering what finger was used when you first used it for that ticket or you are not placing it in the reader the same way you did originally. Personally, I have never had a single problem with it. Basically, you can have no fingerprints at all and it wouldn't make any difference.