I have only had one incident of this nature. My wife and I had multi-day park hopper passes. We went to EPCOT and did the whole scan the ticket and do my fingerprint thing to get in. I went through fine, however, my wife was having issues. It would not accept her fingerprint at all.
The rather gruff CM working the turnstile punched a few numbers on the pad and let her in. Wellllll, we headed over to Soarin' to get a FP and...you guessed it...her card wouldn't work. It said her card was invalid.
We marched back up to the turnstile, found the guy, told him what happened and he just looked at us both like - 'hey, you're in da park heeere..whadaya want from me'. BIG MISTAKE. My 5-foot nuthin wife WENT OFF on this guy (short temper, dosage increased, getting better :lookaroun). I could be mistaken but I think he literally melted into the concrete.
Another CM came over and figured out what happened. The first day we used out passes, my wife used her left thumb. This time she was trying to use her right.
The other CM corrected the issue and off we went. The first turnstile guy quickly disappeared with no apologies or anything.
Bad form, I say, bad form!
I will say, though, we have had no other issues. In general, we have been very lucky!