The Cairo club's doctor Mostafa Al-Monayeri deemed the rising stars unfit to take part in the camp but coach Ramzy said they should be examined by the national team's doctor.
The matter began to escalate when Egypt's doctor said the players' knocks should not prevent them from participating in the camp.
"I only take the report of the national team's doctor into my consideration," former Egypt defender Ramzy, who played for the likes of Werder Bremen and Kaiserslautern in Germany during his playing career, said.
"The doctor told me that Ibrahim's foot complaint and Gaber's injury are minor. I consequently ordered them to remain with the Olympic team.
"I advised them to be committed in order to earn a call up to Egypt's senior team squad in the future but they suddenly left the camp without permission.
"I decided to expel them from my plans. They are no longer part of my team," Ramzy added, without disclosing whether he can recall them in the future.
Attacking midfielder Ibrahim scored Zamalek's winning goal in a last-gasp 1-0 league victory over Masri earlier this week after a brilliant solo effort.
Gaber has established himself as Zamalek's regular right-back after some fine displays, overtaking Ahmed Ghanem who was criticized by the team's faithful for a string of below-par performances.
The White Knights' coach Hossam Hassan recently accused Ramzy, his Egypt teammate for more than a decade, of treating the duo badly.
Shikabala was also involved in a similar trouble with Egypt's senior team coach Hassan Shehata.
Shehata accused the talented forward of feigning injury to skip the Pharaohs' friendly game against Australia last week.