Forty-nine people were sentenced from 3 to 15 years in intensive prison in the same case that led to the killing of three people in July 2013.
Nine defendants were sentenced to 15 years, 20 defendants were sentenced to 10 years and 20 defendants were sentenced to 3 years, court officials said.
Twenty people were acquitted for lack of evidence, they said.
The incident took place in July 2013 in the Canal city of Ismailia when clashes between the Muslim Brotherhood members and the security forces killed three people and injured dozens.
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Badie, 72, the top leader of the now-banned Muslim Brotherhood, was arrested in August 2013 and tried under various charges. He has already been sentenced to life for murder and inciting violence.
The Muslim Brotherhood was designated as a terrorist organisation in November 2013 by the government after the ouster of Islamist ex-president Morsi.
Morsi himself alongwith Badie and 100 other leaders were also sentenced to death in June last year for escaping from prison in 2011. However, an Egyptian court later quashed the death sentence against Badie.