The incident Tuesday happened during a rally that started on Second Avenue and East 25 Street.
A group claiming to fight for Black liberation was involved in several altercations with police Tuesday evening.
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During one incident, plainclothes officers are seen taking an 18-year-old woman into custody, getting her into a van as uniformed bicycle officers arrive to help with crowd control.
Observers on social media likened it to a "kidnapping" by police.
Woman's arrest during NYC protest concerning city officials
Protester Christopher Salata says he knew the woman from their time together during the weeks-long sit in at City Hall Park.
"They grab her off the street as she's skateboarding, don't even put handcuffs on her... that's just terrorism," Salata said.
Video shows controversial NYC arrest of protester
According to police, the suspect, who identifies as a transgender woman, was arrested for past criminal activity in Lower Manhattan.
"The woman taken into custody was wanted for damaging police cameras during five separate criminal incidents in and around City Hall Park," police said. "The arresting officers were assaulted with rocks and bottles."
A law enforcement source says the suspect was wanted for spray painting over the cameras.
Initially, the arrest fueled Twitter rumors, which claimed the woman had been kidnapped.
Plainclothes cops were reportedly looking for known "bad actors" in the protest.
The NYPD calls this a textbook arrest by its warrants squad, which operates in plainclothes to avoid tipping off its targets.
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City leaders took to Twitter to voice their concern over the arrest, including New York City Comptroller Scott Stringer.
Warning: Tweet contains video with graphic language.
New York City Public Advocate Jumaane Williams and council member Carlina Rivera also took to Twitter to express concern regarding the arrest.
The incident added new tension to protests that had largely died down in the city.
However, not everyone agrees with the protesting.
"Enough is enough, it was getting better before George Floyd, but now you're putting the cops' hands behind their back and this is why all the shootings and the crime rate are going up so much," said Benny, who grew up in Brooklyn.
The protest continued around the Madison Park area and made its way to Times Square.
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There were 12 additional arrests in the aftermath of the incident, mostly for disorderly conduct.
One protester damaged the license plate reader on the back of a police car.