The Pharaohs were stunned by Uganda in Kampala after a perfect strike from Emmanuel Okwi on 51st minute gave the hosts all the points at stake to move to top of the log.
"The qualifiers are not over yet, we still have nine points to fight for," Cuper said.
"We tried more than one formation and fielded many attackers, but we could not still get a better result," he added.
Cuper's decision to play Kahraba upfront failed to pay dividends but he says the player will improve in subsequent matches.
"Kahraba is a talented player. He could make a fine strike partnership with Salah. As an out-and-out striker, Kahraba played well in the Africa Cup of Nations in Gabon also.
"The players today had a day off, it's easy to criticize them after defeats. We'll be looking to make sure we make up for our mistakes in the upcoming games," he said.
Ghana will host Congo at the Baba Yara Sports Stadium in the other group game on Friday.
Egypt last played in the World Cup in 1990 while Uganda have never played in the mundial but Ghana have qualified to the last three editions since 2006.