Botswanaian referee Disang Thapelo awarded the home side two penalty kicks, as well as sending off Ismaili duo Sherif Abdul-Fadil and Abdullah Al-Shahhat.
"We will send a complaint to CAF through the Egyptian FA against the Merrikh match referee, we hold him responsible for our exit," club's general manager Abdul-Rahman Annous told FilGoal.com.
Faisal Ajab's first-half penalty kick moved the Sudanese side closer to the competition's final as Ismaili bowed out of the tournament.
Ismaili coach Taha Basri also blasted the referee, despite admitting that the second penalty was correct.
"The referee's mistakes cost us the game, most of his decisions were against us," said the Ismaili manager.
"The first penalty should not have been given, and even though the second one was right, there was no need to re-take it."
Ismaili goalkeeper Mohamed Sobhi managed to save the retaken penalty twice, but he failed to stop Ajab's first one, which proved to be enough.