The Red Devils lost 2-0 in a game that witnessed the sending off of the club's coach as well as skipper Ahmed Al-Sayed, two incidents that angered Al-Badri.
"Throughout the whole game the referee was very rough with my players and quite soft with Leverkusen," Al-Badri told Ahli TV.
Al-Badri's sending off resulted in a 15-minute delay to the second half as Leverkusen manager Rudi Voller intervened to calm down the tactician.
Football director Hadi Khashaba echoed Al-Badri's comments, adding that his players didn’t know how to deal with the referee's injustice.
"The referee was unexplainably nervous despite the fact that it's just a friendly game," Khashaba said.
"He (the referee) should have been fair and not shout at my players upon making some decisions."
Watch Al-Badri speak to Ahli TV