Botswana's Player of the Season, Edwin Olerile, and the Supporters' Player of the Year, Skhana Koko, have been left out of Stanley Tshosane's 23-man squad, much to the surprise of Batswana fans.
The coach named his squad on Sunday, and they departed this morning for Yaounde, Cameroon, where they will camp ahead of travelling to Gabon, having cancelled a camp in Qatar at the last minute because of funding problems.
The players had refused to train on Thursday and Friday, but did play a scheduled friendly against Zimbabwe on Saturday, which ended 0-0.
The country's president had also called on the team to "put the nation's interest" ahead of their own.
The payment row began in December, when the players demanded 100,000 Pula (+/-R108 000) from the Botswana FA for every member of the final 23-man squad, plus a R16 000 bonus per win, and R8 000 per draw for the group stages.
The squad also asked for a P35,000 (R38 000) incentive for each player should they progress to the knock-out stages, and an increase in their daily allowance from P100 (R108) to P500 (R540) per night.
SuperSport United's Dipsy Selolwane told the BBC: "It's disappointing that at the last minute before we travel, players are still uncertain about the bonuses.
"As much as [we were asking for] a small amount of money, they should be able to manage it without blinking but that proposal was turned down and we were given an ultimatum that either we stay or we go home.
"So we feel that we were not treated right."
But on Sunday Botswana's President Ian Khama urged the players "to put the nation's interests ahead of their own".
SuperSport's Mogogi Gabonamong, a leading figure in the Botswana national team, apparently had a private meeting with BFA CEO Duncan Kgame, Khama and Minister of Sport Shaw Kgathi before the squad departed.
Today, BFA president David Fani told The Monitor: "We will issue a statement how the players would be remunerated, we think the issue has been addressed but rather wait for the staement."
Meanwhile, Tshosane has included injured captain Mompathi Thuma in his final squad for the Nations Cup, but has left out speed merchant Skhana Koko, who has been in a similar situation.
Koko is touted as the next big thing in Botswana football, and his omission has disappointed and surprised the country.
Botswana squad: Goalkeepers: Modiri Marumo (Bay United, South Africa), Noah Maposa (Gaborone United), Kabelo Dambe (Rollers)
Defenders: Mompathi Thuma (BDF XI), Ndiyapo Letsholathebe (Police XI), Musa Ohilwe (Gaborone United), Mosimanegape Ramohibidu (BMC), Monametsi Kelebale (NICO), Tshepo Motlhabankwe (Mochudi Centre Chiefs)
Midfielders: Mogogi Gabonamong (SuperSport United, South Africa), Joel Mogorosi, Pontsho Moloi, Othusitse Pilane (all Mochudi Centre Chiefs), Boitumelo Mafoko (Santos, South Africa) Ofentse Nato (Gaborone United), Phenyo Mongala (Bloemfontein Celtic, South Africa), Patrick Motsepe, Tshireletso (BDF XI), Mogakolodi Ngele (Rollers)
Strikers: Jerome Ramatlhakwane (unattached), Diphetogo Selolwane (SuperSport, South Africa), Onalethata Tshekiso (Rollers), Moemedi Moatlhaping (Bay United, South Africa)