Nigeria said no reason was given for their plane being sent to Al Abraq, about 230km (143 miles) away from Benghazi, and they were not met by an LFF representative on their arrival on 13 October.
Players posted on social media that they had been left without food, wi-fi or anywhere to sleep, and the Super Eagles squad returned to West Africa the day before the game.
Meanwhile, Libya raised complaints that their squad had received poor treatment in Nigeria ahead of the reverse fixture on 11 October, which the hosts won 1-0.
Caf stepped in and cancelled the tie in North Africa, and a disciplinary board decided that Libya had breached two articles of its disciplinary code as well as an article of the Africa Cup of Nations regulations.
The breaches related to principles of conduct, security for the organisation of matches and accommodating visiting teams.
At the time, Troost-Ekong described the treatment Nigeria received as “mind games” – but the LFF denied suggestions of foul play.
Ahmed said Caf “did not evaluate the real situation”.
“The plane’s course was changed for technical and logistical reasons related to air navigation,” he added.
Nigeria’s foreign minister Yusuf Tuggar told Newsday on the BBC World Service that the situation was “most unfortunate” and complicated by the fact Libya is split between two administrations which both claim to be the country’s legitimate rulers.
“Our team flew into a part of the country that was under the control of a government that did not have diplomatic representation in Abuja,” he said.
The 3-0 walkover means Nigeria are one victory away from reaching the 2025 Nations Cup in Morocco.