There are now allegations that professional protesters were used in those fights. While professional protesters aren't anything new on the national stage, locally it's a different story. And Trump supporters aren't amused.
Earlier Tuesday, the district attorney's office filed charges against one of them, who is accused of throwing a metal barricade at a police officer.
"He was released on the supervised own recognizance program, which means he'll be surprised by the pre-trial services department, but without bail being set," said Santa Clara County Deputy District Attorney Chris Boscia.
Mayor Sam Liccardo says there's no room for violence in this city.
"Donald Trump rallies have been marred by violence in many, many cities," he said. "And these are great challenges that major city departments have to grabble with."
One high profile Trump supporter claims so-called "professional protesters" may have also had something to do with the violence.
Former political advisor Roger Stone believes that some people are getting paid to cause a ruckus at political rallies.
In a Skype interview he said, "In fact, one of those in San Jose was a protester seen only days ago outside Trump Tower in New York. That's a highly mobile protester."
A woman pictured standing next to a burning Trump hat has been photographed at multiple protests.
Stone says others have also been responding to Craigslist ads in multiple cities across the country, asking for people to protest against Trump.
"It makes national news," said Stone. "And their message of 'Trump is bigot Trump is a racist' resonates in a way that would discredit his candidacy with left of center voters."
The San Jose Police Department is following up on leads and says more arrests are possible.