Parents also claimed that white children were allowed to opt-out of the exercise, while children of color were not.
Police said they believe there could be more victims connected to the case in upstate New York.
The popular holiday song is one of several that have been removed and replaced with "more contemporary" and "relevant" content.
"The charges outlined in this case are as heinous and disturbing as they come," New York Attorney General Letitia James said.
On Friday, Mayor Lovely Warren declared a state of emergency due to the rise in gun violence. The city has already seen 71 homicides this year.
The former Rochester police chief is running as a member of the GOP citing a number of issues within the Democratic Party that he no longer supports.
Officers say a man in his eighties fatally shot himself and his partner on Saturday in an "extremely tragic event."
Police in Rochester, New York, said hundreds of people were in the parking lot of a Walmart when gunfire erupted.
Timothy Granison has pleaded not guilty to two counts of criminal possession of a controlled substance and one count of criminal possession of a firearm.
Warren is currently under indictment on felony campaign fraud charges with the case pending in state court. However, the Monroe County District Attorney's office said Wednesday's police search wasn't connected to the campaign finance charges.
Protesters gathered in Rochester, New York after it was announced that a grand jury had declined to indict the officers involved in Daniel Prude's death in March last year.
Protests have been held outside Rochester Police Department's headquarters after body camera footage of the incident was released on YouTube.
Body camera footage of the incident on January 29 shows officers restraining a distressed girl as she repeatedly screams for her father.
Demonstrators arrived at the building in downtown Rochester to protest against the earlier arrest of a man, who police conceded had been taken into custody on an "erroneously issued" bench warrant.
"We have a pervasive problem in the Rochester Police Department, one that views everything through the eyes of the badge and not the citizens we serve," Mayor Lovely Warren said.
U.S. Attorney James Kennedy announced the charges during a press conference in Rochester, New York, on Wednesday afternoon.
Demonstrations of persisted in Rochester as an investigation into the death of Daniel Prude during a March arrest continues.
Protesters gathered hours after Police Chief La'Ron Singletary and his entire command staff announced their retirement amid criticism over the handling of Daniel Prude's death.
Rochester Police Chief La'Ron Singletary will resign after 20 years of service, saying he he won't sit idly by while people attempt to destroy his character.
A spit hood, which is designed to protect police from saliva, was placed on a naked Prude's head by Rochester Police officers while they detained him on March 30.
Petitions have been set up both in favor of and in opposition to a high school assistant principal who yelled "f**k the police" at a Rochester, New York, protest Friday evening.
Protests raged for the fourth straight night in Rochester, New York in response to the release of the video of Daniel Prude's death in police custody.
On social media the owners of Swan Dive invited the demonstrators in for refreshments, shortly before the eatery was vandalized and its patrons harassed.
Video footage shows dozens of protesters, chanting "Black lives matter," climbing up the stairs of a restaurant as patrons dining outside look on.
The hospital has offered to speak to Prude's family and answer any questions they might have about his treatment.
Prude, a 41-year-old Black man, died on March 30 following an interaction with Rochester, New York police officers. His death was ruled a homicide by Monroe County Medical Examiner's Office.
An autopsy report ruled Prude's death a homicide, with "complications of asphyxia in the setting of physical restraint" listed as a cause of death.
Daniel Prude died in March, seven days after Rochester police placed a hood over his head and drove his face into the ground.
Incumbent Monroe County, New York county executive Adam Bello is the first Democrat to obtain the seat in 30 years. Now the Republican-controlled county legislature is allegedly seeking to limit his powers before he enters office.