The players had on Tuesday refused to leave their hotel rooms and missed their flight back home due to non-payment of match bonuses and allowances.
Also, there were insinuations that coach Paul Aigbogun collected money from the players before inviting them for the youth fiesta, a claim which the NFF has dismissed.
Speaking about the team’s outing in Poland, Babayaro who won the 1996 football gold medal at the Olympic Games in Atlanta, said the side performed abysmally.
“From the beginning, their performance has been poor. Our exit was expected, it was long-coming,” Babayaro told Vanguard.
“Look at how we qualified in the first instance, apart from the very first game we won and we won against a very poor side, we never beat any other team.
“The technical team are not up to speed technically. It baffled me that we will be going for a World Cup without our best legs, it is a shame.
“If we play well with the youngsters and we are eliminated in the group stage it’s cool, it is developmental. We need to go for the right lads for our own future.
“The NFF should do the needful. Do your proper investigation into what happened with the Flying Eagles. How can we be taking mediocre players to the competition like the World Cup and then dropping the best players?”
He added: “the team should be investigated and if the coaches are found wanting they should be sanctioned to serve as a lesson to others.
“They are killing our future, the purpose of the tournament is to create room for the young kids who will graduate to U23 and then to the Super Eagles.
“Our coaches need orientation, they should select the right ages. The NFF should not put the coaches under pressure, pay them well when due, that way if you find them trying to involve in any illicit behaviour as regards team selection then it is easy to deal with them because you have given them everything to work.
“What stops us from taking the right players to the tournament? The coaches need to be orientated that they should not use their selfish interest to bring the nation down.”