This situation is ridiculous. She wouldn't have been able to get to the airport's non-Schengen area from the airport's Schengen area and do what the airline agent mentioned unless at least one of two things happened: the passport control officials or machines failed to prevent her from crossing the airport's Schengen border; or there was an ID or passport swap inside the non-Schengen area of the airport. It seems the latter situation is what has the airline agent being uptight.

If it were me and if I could afford to be denied boarding, I would call their bluff and document what they said and did along with making sure to have evidence that they denied me transport while I clearly had possession of my valid passport.