They were detained on Saturday and are currently in custody assisting police with their inquiries.
The teenagers, aged 15 and 18, have been arrested on suspicion of riotous assembly on the Albertbridge Road.
The 20-year-old man was held on the lower Newtownards Road on suspicion of disorderly behaviour and provocative conduct.
Meanwhile, a PSNI spokesperson said a flag protest passed without incident in Carrickfergus, Co Antrim where a road block was cleared by police.
Earlier around 600 protestors staged a flag protest at Belfast City Hall amid a heavy police presence.
They had made their way to the city centre for the seventh week since the dispute began following a vote to restrict the number of days the Union flag flies over city hall to 18 designated days.
A large number of police landrovers lined the area around city hall and the protest passed off without incident.
Later protestors returned to east Belfast via Middlepath Street and the Lower Newtownards Road near the Short Strand interface. The Albertbridge Road and Castlereagh Street areas were closed for a time in the afternoon before crowds dispersed.
The flag protest in east Belfast has now ended and all roads have been reopened to traffic.
Police said neighbourhood policing teams were involved in patrolling the interface.
"The area was quiet and we will continue to provide attention to these areas," a PSNI spokesperson said.
Last week, severe rioting broke out in east Belfast following violent clashes between loyalist and nationalist crowds in the Short Strand area.
Sunday will see the Union flag fly at City Hall on one of the designated days to celebrate the Countess of Wessex's birthday.