Yes, about 15 years ago on a LH flight from FRA to ORD and then UA to SEA. I got through passport control and was at the gate with about 15 minutes before boarding started and suddenly noticed that I was seated somewhere far from where I would have chosen. I then checked my connecting flight and not only was it in the middle way down the back, it was to New Orleans! I have a hyphenated last name so you'd think that would lessen the chances of a mix up but sure enough, instead of "ISGONE/TED" I was checked in as "ISHERE/THOMAS". The gate agent was confused at first and then saw the similarities in our names and printed out my boarding passes. I didn't ask if "Thomas" checked in as me but I suppose he must have because I'm not sure they would have checked me in so close to boarding.