Cairo (CNN) -- Predawn gunfire and clashes from a violent military crackdown on protesters in Cairo's Tahrir Square on Saturday left Egyptians feeling shocked, confused and angered in the hours that followed.

Long bursts of machine-gun fire erupted overnight starting around 3 a.m., when scores of soldiers backed by armored personnel carriers launched a raid on the square.

Amateur video posted on YouTube showed troops storming the square's central roundabout amid rattling gunfire.

Hundreds of protesters -- calling for Egypt's ruling military council to prosecute former president, Hosni Mubarak -- fled the scene as clouds of tear gas billowed through central Cairo. Among them were at least four wounded and bleeding men. Protesters tried to stop an ambulance from leaving the square.

Two badly beaten men in military uniform were lying in the back of the vehicle. It is not clear whether or not they were troops engaged in the crackdown -- or whether they were some of the 15 uniformed army officers and soldiers who defied direct orders by joining a protest of tens of thousands of demonstrators in Tahrir Square on Friday.

By morning, security forces withdrew from the square, leaving behind spent bullet casings and in one place, a pool of blood.

Egyptian military confirmed that one person died from a gunshot wound overnight and that 42 people were detained, including three foreigners.

"It was a disaster," said protester Shadi Essam. "The army attacked us in coordination with the police."

Essam said activists tried to help the dissenting military personnel to escape the crackdown by dressing four of them as civilians.

Gen. Adel Amara, a member of the Supreme Council of the Armed Forces, said security personnel did not attack the protesters.

"Because of the pushing and clashes between the armed forces -- who I assure you had no weapons whatsoever -- because of clashes and pushing and shoving and you can imagine how a big group of protesters and soldiers could get some bruises in the pushing and shoving. Four from the armed forces (who joined the protesters) have some bruises plus nine civilian protesters," he said.

Tensions mounted between demonstrators and the military hours before the raid. Late Friday, activists were seen confronting two military officers who tried to approach the square's central traffic circle. Demonstrators shoved the officers, knocking their hats off their heads, and then pursued them as they fled the square.

By daybreak, the military had withdrawn from Tahrir. Lines of barbed wire and several burned-out trucks blocked vehicle traffic from entering the area.

The clashes came a day after large crowds of protesters amassed at Tahrir Square, many of them angry with Egypt's new military rulers. After Mubarak's ouster in February, the military took control -- riding a wave of popularity for refusing to fire on pro-democracy protesters during 18 days of anti-government protests.

But in the weeks since, the secretive 20-man council has produced increasing frustration and criticism from different portions of the Egyptian political spectrum. Critics have complained of human rights abuses and lack of transparency in the council's decision-making process.

On Friday, some soldiers joined the protests in a direct challenge to Egypt's military rulers. For long intervals, they took to one of the stages erected in the crowded square and called for the country's military rulers to be replaced.

"If they really wanted to prosecute these corrupt officials they would have done it immediately. That's why we are here today," one of the protesting officers said during the Friday protests.

Earlier this week, several military officers took to the Internet, recording video statements accusing the chairman of the ruling council, Field Marshal Mohammed Tantawi, of protecting Mubarak from prosecution and of leading a counterrevolutionary movement.

"He should step down. He makes stupid moves. He did not learn from the mistakes of the last 60 years. Military should not run countries," said Mohamed Ibrahim Garib, who makes a living importing and exporting clothing, on Saturday.

Tempers flared at one point between soldiers and citizens outside the gates of the Egyptian Museum, which has been used in past months as a detainment center by the Egyptian military. An officer fired shots in the air, prompting angry youths to mob the gates and hurl stones into the museum compound. After several minutes, the confrontation subsided.

The military issued a communique Saturday morning, accusing a former member of Hosni Mubarak's long-ruling National Democratic Party of "inciting people in Tahrir."

The military announced it had issued arrest warrants for NDP member Ibrahim Kamel and several of his associates, after accusing them of being "present in Tahrir Square after curfew as thugs and scaring the citizens."

In scenes reminiscent of street protests last January and February, activists have once again blocked entry into Tahrir, using coils of barbed wire apparently left behind by the military.

CNN's Ivan Watson and Mohamed Fadel Fahmy contributed to this report