By Eric Marrapodi and Miguel Marquez, CNN

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Copacabana Beach, Brazil (CNN) - Don't blame the pope's Swiss Guards if they had nightmares Monday night. There was plenty to disturb their sleep: a mobbed motorcade, a bomb scare and protesters clashing with police.

When Pope Francis arrived here Monday for World Youth Day, a weeklong Catholic event held every few years, the massive security effort was temporarily undermined by a traffic jam.

As the papal motorcade was driving from the airport to the presidential palace, federal officials steered the motorcade into the busiest of several potential routes. As the motorcade slowed, papal admirers swarmed the silver Fiat hatchback carrying Pope Francis, reaching into his open window to touch the pontiff.

A Vatican spokesman said the pope wasn't afraid - but his secretary was.

“The Pope’s secretary told me that when the car was stopped, he was scared at times, but the pope was very happy and waving,” said the Rev. Federico Lombardi.

Brazilian officials blamed the mob scene on miscommunication between the city of Rio de Janiero and federal police. Lombardi simply said the motorcade had taken a wrong turn.

Still, the pope’s security team was confident enough during the stoppage that Domenico Giani, the Vatican's chief of papal security, opened the pope’s door and handed him a child to bless.

Once Francis transitioned into the open-topped Popemobile, he moved easily through the tens of thousands who filled the streets of Rio to catch a glimpse of the new pontiff - the first pope to hail from Latin America.

The pope’s regular contingent of Vatican security, including the Vatican police and the Swiss Guard, moved with the pope in the streets, occasionally bringing infants over the barricades to meet the pontiff.

There was a different scene shortly after Francis met with Brazilian President Dilma Rousseff at the Guanabara Palace. Protesters - who had promised to be out in force during the papal visit - clashed with police in riot gear.

Police said the protesters hurled rocks at them and they responded with water cannons and tear gas. Six arrests were made and two photographers were injured.

The Brazilian police also said in a statement that on Sunday they had discovered a small homemade explosive device at a shrine to the Virgin Mary in the city of Aparecida the pope is scheduled to visit later this week. The small plastic, duct-taped device was destroyed.

READ MORE: Explosive found near site pope plans to visit

State of Rio de Janieo security officials met on Tuesday to find out what went wrong and how to fix it.

The Brazilian Ministry of Defense said they have deployed more than 20,000 military and police forces to deal with security for the weeklong event.

For the final Mass, in a large field west of Rio, the defense ministry said 400 soldiers will be stationed at the altar and 94 observation towers in the crowds, which officials say could top a million people.

"Logistically, (it is) the most complex event that the city ever faced," Rio Mayor Eduardo Paes said. "We know that the pope likes to bend ceremonial rules, but that is more than welcome in Rio."

READ MORE: Pope Francis embarks on historic trip to Brazil

On Tuesday, bomb-sniffing dogs and police swept the main stage at Copacabana checking the altar and the VIP seating area. Three small Brazilian navy ships were sweeping along the shore, staggered out for several miles, maneuvering up and down the coast.

The pope was scheduled to rest on Tuesday. The formal program for World Youth Day begins Tuesday evening.

CNN's Hada Messia contributed to this report.