The volatile situation prompted US authorities to close the San Ysidro port of entry, the busiest crossing along the US-Mexico border, for six hours.
San Diego Sector Chief Patrol Agent Rodney Scott told CNN Monday morning that the 42 people, mostly men, were arrested Sunday on the USA side of the border.
"As the events unfolded, quick, decisive and effective action prevented an extremely unsafe situation", he said.
While arguing Monday that the use of tear gas on hundreds of migrants and asylum-seekers near the US border the previous day was justified, a Fox News commentator asserted: "It's natural".
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By doing so, "within a couple days or a week", Cabrera said, "we would see a much smaller number of people actually claiming asylum".
President Trump threatened to shut the 2,000-mile (3,200km) US-Mexico border down once more this morning.
"What we saw over and over yesterday was that people would purposely push women and children to the front and then begin basically rocking our agents", said the border chief, Rodney Scott.
Department of Homeland Security Secretary Kirstjen Nielsen has promised to maintain a "robust" presence along the border to block the migrants from entering the U.S. "DHS will not tolerate this type of lawlessness and will not hesitate to shut down ports of entry for security and public safety reasons", she said in a statement.
The clash between the migrant caravan and USA authorities along the Mexican border in recent days highlights a contentious topic in the immigration debate: asylum laws. "Nobody's coming into our country unless they come in legally".
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Large groups of migrants have tried crossing the border before, with a group of more than 100 clashing with Border Patrol agents in November 2013. "Congress, fund the WALL!". They only retreated when authorities deployed tear gas, which is said to have been felt almost a mile away. "But the truth is the majority of the people that are part of this caravan...are men", Schwartz said while reporting live from a camp that members of the caravan set up in Tijuana, Mexico.
Many hope to apply for asylum in the USA, but agents at the San Ysidro entry point are processing fewer than 100 asylum petitions a day.
However Mr Trump, the United States president, and government agencies involved defended the response and insisted on the need to secure the border with Mexico.
Over the weekend, the scene at the border devolved as members of the current migrant caravan attempted to storm the border wall between Tijuana and San Diego, and threw rocks at law enforcement and military officers lining the border.
"They know they're taking advantage of the system, and they know there is nothing we can do about it", said Cabrera.
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Mexico's Interior Ministry said Sunday the country has sent 11,000 Central Americans back to their countries of origin since October 19, when the first caravan entered the country.