Dozens of unaccompanied minors were left in the “Jungle” camp in Calais overnight, despite French officials declaring the camp now empty.
Aid workers say about 100 young people slept rough, but the head of the regional government said it was 68.
Fabienne Buccio also claimed some of those who remained overnight were not originally from the “Jungle” camp.
Nearly 5,600 people have been moved to reception centres since Monday, the government said (in French).
This includes about 1,500 unaccompanied minors being housed in an on-site container camp, which activists say is now full.
The camp has become a key symbol of Europe’s migration crisis, with its residents desperate to reach the UK.
Demolition crews are continuing to clear remaining tents and shelters from the area, which were damaged in fires reportedly set by departing migrants.
Caroline Gregory of Calais Action, a British charity, said about 100 unaccompanied children had been left in the camp overnight.
“We were begging the French authorities to actually do something about the refugee children and nothing was done,” she told the BBC on Thursday.
Volunteers found shelter for the children in a warehouse where many of the migrants were being processed, as well as a makeshift school inside the camp.
Some of the youths slept on the ground outside one of the centres that was being used to register migrants for relocation over the past three days.
“I spent the entire night here,” one young Afghan told the AFP news agency. “I am in the queue for minors to go to England. I have family there.”
French police, meanwhile, say they are still finding migrants in shelters who do not want to leave.
Ms Buccio, the prefect of the Pas-de-Calais region, said that those who had slept in the camp overnight had travelled from other parts of France.
She had earlier declared the operation “mission accomplished”.
The 68 children found will be moved to centres elsewhere in France, she continued, but there will be no more buses to take migrants to reception centres.
The camp could not become a magnet for anyone who wants to get a place in the centre, she warned.
She said the site would be completely cleared by Monday.
The UK Home Office said French authorities were responsible for “all children in Calais during the clearance operation – including those being assessed for possible transfer to the UK”.
Fires have been lit during the clearance work this week – one man was reportedly injured when a gas canister exploded in the flames.
More than 1,200 police officers have been deployed for the clearance operation. The camp is unpopular locally and has required a large security presence to prevent migrants reaching the UK on lorries or trains heading across the Channel.
Since the start of the week, French authorities have been bussing thousands of people to shelters and centres where they will be able to seek asylum.
A total of 5,596 people, including children, have been transported from the Jungle for resettlement, the French government says. This includes 234 minors brought to the UK since last week.
The camp had an estimated 6,000-8,000 residents. Authorities fear they will return to set up camp again once the clearance operation is over.
The Jungle camp is near the port of Calais and close to the 31-mile (50km) Channel Tunnel
Officially about 7,000 migrants live in the camp. The Help Refugees agency said the final population ahead of its demolition was 8,143
The camp was halved in area earlier this year but the population continued to rise, and reports of violence have increased
Many migrants attempt to hide themselves in cargo vehicles entering the Channel Tunnel
The area has been hit by protests from both locals and truck operators