I once was checked in under another passenger's name - same last name, different first names - with Airtran at MCO. This was not too long after 9/11 when you had show BP and photo ID twenty thousand times between the check-in counter and the gate (including as you boarded). So at least 3 people supposedly checked my BP against my ID, and my BP was scanned, never catching the error. (I never paid attention either, obviously)
It wasn't until the person whose name was on my BP arrived at my seat, with me in it, that we knew there was a problem. It took about 5 minutes to sort it out, luckily my seat hadn't been given away since I had never "checked in" prior to the cutoff time and it was, (to quote every GA on every flight) "a
very full flight"
Nothing is foolproof I guess.