Most likely scenario would be that the agent had both PNR's on the go when you were reserving, closed them to ticket the one you thought you had, and then wound up cancelling the wrong one, later.

Fortunately, with a paper ticket, what the ticket says trumps what the computer says. You have clear evidence of buying a ticket, subject to the fare rules in place at the time, for the routing appearing on the face of the ticket. With an e-ticket, you don't have that same level of certainty, since what is in the computer may 'change.'