I had it happen once @ LGA with American Eagle. They pre-boarded an elderly/disabled pax ahead of time. With a few puddlejumpers on the tarmac, I guess the GA brought her to the wrong aircraft. The error was apparently caught after the wheelchair passenger was aboard the plane; this was explained to us as the reason for the delay in boarding, although it did not (significantly) affect depature time.

Mreover - recently I was flying on Horizon and a fellow with a NW codeshare ticket told me that he had been assigned my seat. I looked at his bp; I knew I had the right seat myself, but couldn't find his correct seat. The FA found it in another (less conspicuous) spot, but I didn't blame him for thinking he was in my row from what I saw.