The Irish Football Association look certain to demand answers from FIFA after another youngster decided he would rather play for the Republic of Ireland.
Manager Nigel Worthington believes there could be flaws in a system that allows players who have come through the age groups with one nation to represent another country.
Worthington has failed in his attempt to persuade promising Everton defender Shane Duffy his long-term international future lies with the province.
Instead the 18-year-old has withdrawn from the squad to face Albania in a friendly on March 3.
Duffy’s decision to switch allegiance to the Republic follows those of Manchester United midfielder Darron Gibson and Portsmouth defender Marc Wilson.
Wilson has been named in the Republic squad for the first time as they prepare to meet Brazil.
Duffy progressed to the under-21 side after captaining the under-19s.
Worthington told the BBC: “There is a loophole, where a player can walk away after a lot of time and investment has gone in. Until it’s resolved, that’s where we are.
“Shane has represented Northern Ireland all the way through from a very early age to the under-21s.
“I am a big admirer of Shane. I like him as a player and a lot of work has gone in with different coaches. I am disappointed with the situation as he is going to be a very good player.”
Duffy decided about three months ago he wanted to play for the Republic but Worthington said he and his manager David Moyes managed to persuade him to stay put.
However the Derry-born player, who has made two Europa League appearances for Everton this season, had another rethink.
He confirmed to Worthington he was no longer available for selection for Northern Ireland after being named in the squad for Tirana.
Duffy looked set to win his first cap in the absence of skipper Aaron Hughes and his Fulham team-mate Chris Baird, who are both rested.
Worthington added: “Shane has now decided after discussing the matter with his family to represent the Republic. As a manager I have got to respect that.”