Earlier up to 2,000 people took part in a loyalist protest outside Belfast City Hall, which has stopped flying the union flag every day.
There was trouble on the Newtownards Road after and some minor disturbances on O’Neill Road in Newtownabbey. Both areas are now quiet.
The police have said paramilitaries have organised some of the violence.
Bricks and other missiles were thrown at police officers and a car was set on fire in east Belfast.
An attempt was made to hijack a bus in the Castlereagh Street area. Public transport company Translink has said there are some disruptions to services due to protests.
Police have charged a 15-year-old boy with riot and criminal damage over the trouble in east Belfast. He is to appear before the city’s youth court on Monday.
A 32-year-old has been charged with disorderly behaviour and resisting police in the Donegall Square West area of the city centre. He is to appear in court in the New Year.
In Belfast on Friday, eight officers were injured and 13 people arrested in clashes between loyalists and police.
There was also trouble in Newtownabbey on Friday, bricks and other missiles were also thrown at police on the O’Neill Road. Eight people have been charged with public order offences in relation to this.
Loyalists opposed to new restrictions on flying the union flag at Belfast city hall have been holding protests across Northern Ireland all week after the city council voted to fly the flag on about 20 designated days.
Nationalists at Belfast City Council had wanted the union flag taken down altogether, but in the end voted on a compromise from the Alliance party that it would fly on designated days.
Unionists have said they consider the changes regarding the union flag to be an attack on their cultural identity and there have been protests in different parts of Northern Ireland since it was taken.
There was also a small protest at a football match in County Fermanagh on Saturday. Demonstrators took to the pitch at half-time during the Irish League game between Ballinamallard and Belfast side Linfield.
The protest at Belfast City Hall was peaceful, but an Irish tricolour was set on fire.
During the protest the crowd was addressed by former BNP member Jim Dowson.
“Stripped away”
The Progressive Unionist Party leader Billy Hutchinson and UDA boss Jackie McDonald were also present.
Mr Hutchinson said it was unfortunate that tricolours had been burned.
“It is unfortunate that some people feel that they have to do that. This is about Northern Ireland and Northern Ireland republicans.
“They are venting their frustrations against republicans in Northern Ireland.”
One of the demonstrators, Johnny Harvey, said his heritage was being “stripped away”.
“We’re here first and foremost to protest against the removal of our union flag from the City Hall, but basically that just scratched the surfaces of the problem here in Northern Ireland and the fact that our whole culture, heritage and traditions are being stripped away from us bit by bit,” he said.
Assistant Chief Constable Will Kerr, of the Police Service of Northern Ireland, welcomed the fact the protest at the City Hall passed off “largely peacefully”.
“However, let’s not forget the fact the Christmas Market had to be closed temporarily and traders both in the city and indeed elsewhere have felt a massive impact as a result,” he said.
“As is the risk with all large protests, we saw elements of the protest start to engage in disorderly behaviour as they returned to their respective areas of the city.
“This is the obvious consequence of bringing people out onto the streets at a time of heightened tension. Those involved in the protest should reflect on their own responsibility for any associated disorder and violence.”
The home of an Alliance party councillor was attacked in County Down overnight.
The party said windows were smashed and a car also damaged at Linda Cleland’s house in Newtownards.
“I saw this tall hooded person in my garden – I have a rockery – and they were lifting the boulders,” Councillor Cleland said.
“There were more bangs and I heard people on the roof and then I phoned 999.
“They’ve literally put in all my downstairs windows, they’ve put in all the windows of my car and they’ve put in one of my upstairs windows. I have never been so scared in my life, or felt so helpless.”
Politicians have warned that the economy is being damaged by the protests, on what should be some of the year’s busiest shopping days, and have appealed for them to stop.
