It was reported that Hassan had row with Al-Bardi in the dressing room but Ahli football director Hadi Khashaba ended it in no time.
The Egypt skipper said sorry for his inappropriate reaction, according to a statement on Ahli's official website.
"Hassan assured that he fully respects Al-Badri and all the coaching staff members," the statement reads.
"He also stressed that he didn't mean to object to Al-Badri's decision, but only wanted to play the whole 90 minutes in order to hit peak form ahead Wednesday's game with Zamalek in the round of 16."
Ahli set up a cup meeting with their arch-rivals Zamalek upon sinking lower division side Nabaroh.
A month ago, Hassan refuted reports suggesting that his relationship with Al-Badri was strained after kicking an icebox while walking off the pitch in the league Cairo derby.