I got this on my last Ex-DUB as my flight had been re-ticketed due to a UUA. I'm a dual US-Swiss, so I have to swap passports depending on if I'm flying to the USA or not. My entered passport information had dropped out. Putting that info back in fixed my problem, but not that of Mrs. greg5 who's only Swiss.
Check in at the airport was a non-issue. Agent says that it always happens. Though this didn't happen to us last year.