my case was even more embarrassing - i had a burgundy passport in hand which has “European Union” (in the language of the issuing country) written on the cover. Yet, the gate agent claimed that the issuing country “cannot be in the EU”, and demanded to see my Schengen visa. It was all rather demeaning, station manager was called, who very soon realized the error, apologized and brought me to the plane. Probably mentioned sth to the purser, because I got the J meal then