The players refused to train yesterday, as they prepare to face Burkina Faso in crucial back-to-back Africa Cup of Nations qualifiers.
The BFA was engaged in talks with the players yesterday, which the mother body's spokesperson, Tumo Mpatane, described as progressive, as the two sides sought a breakthrough in the deadlock.
The players wanted to be paid allowances from previous games, before they could resume preparations for the trip to Oagadougou.
"There has been a way forward. The BNSC (Botswana National Sport Commission) has paid the players appearance fees from Angola and the Independence Day match (against Namibia). The money has been transferred to their accounts," Mpatane said.
"Please allow me to convey my apology for what I did during the national team call up that resulted in me being dropped from the national team. My behaviour was extremely inappropriate, immature and lacked the respect for Botswana football, the national team, Galaxy and football supporters. It was bad behaviour I regret," Ditsele said.
"It was embarrassing and I learnt that nobody appreciated my behaviour. In future, I have every intention of curbing my thoughtless actions and learn to adjust my behaviour befitting the Galaxy and football in general. The embarrassment I have caused to Galaxy is highly regretted."
Zebras coach, David Bright is expected to address the issue when he faces the media before the team's departure for Burkina Faso.