A month prior to kick-off, the four-time champions were engulfed in controversy following the retirement of veteran striker Asamoah Gyan from international duty, after he was stripped of the captaincy in favour of Swansea City attacker Andre Ayew.
The forward would, however, rescind his decision but only after a plea from Ghana President Nana Akufo-Addo.
At the championship, the Black Stars won just one of four games played and suffered a Round of 16 elimination, their first time of failing to make the quarter-finals since 2006.
“I told Kwesi Appiah before he left for the tournament that we could not win the trophy," Manu told Storm FM.
"He called me after he came [back from the tournament] and I told him how politicising things in the team affected them and that we couldn't win the trophy because our football is mingled with politics [involving the opposition political party National Democratic Congress (NDC) and the ruling New Patriotic Party (NPP)].
“[I also told him before the tournament]: 'I have heard that you have stripped Asamoah Gyan of his captaincy and he explained but I told him he didn’t act well.
"'They did this to you in 1992 when you were stripped of the captaincy and handed it over to Abedi Pele because you couldn’t speak french when we were going to Senegal [for Afcon] which brought a lot of problems to the team'."
Appiah's stay as Ghana coach has been thrown in doubt following the disappointing Afcon performance.
The GFA Normalisation Committee is yet to make an official statement on his future.