Earlier in the day, a large group marched along Manhattan's Fifth Avenue, chanting "Count every vote!" as several states continued to tally outstanding ballots, New York's WABC-TV reported.
This election cycle, millions opted to mail their ballots instead of voting in person amid the coronavirus pandemic.
The macrhers headed from the New York Public Library in Midtown toward Washington Square Park in Greenwich Village after President Trump's team announced the filing of a series of lawsuits in Michigan and Pennsylvania to halt the vote count in those states.
The protest was peaceful and eventually dispersed. However, some people returned, setting fires and engaging in other destructive behavior, the news station reported. The NYPD reminded New Yorkers that officers would not tolerate illegal activity.
"We support everyone's right to self-expression, but setting fires puts others at risk and will not be tolerated. We are working to de-escalate the situation near Morton Street in the West Village to prevent further damage from occurring," the NYPD tweeted.
Videos posted to social media showed protesters being arrested and violently clashing with police. Police confiscated several weapons, including knives, a stun gun, and M80 firecrackers.
The NYPD said it made about 50 arrests during the protests, according to Reuters. Police Commissioner Dermot Shea said officers arrested someone breaking into a store window and put out fires.
In a tweet, the department said it had formed a Looting Task Force to deal with just that.
Businesses in cities across the country boarded up their windows ahead of Election Day over fears of the kind of unrest that raged over the summer.
Nationwide, most of the demonstrations related to the election have been peaceful.