Dozens of children have reportedly been forced to sleep on the roadside of the Calais Jungle, despite French officials declaring the clearance complete.
Images showed youngsters lying on blankets in the dirt, after allegedly being turned away from the part of the camp where they had been staying for safety.
On Thursday morning, volunteers said "at least 100 children" were queuing for a registration process which had been ended on Wednesday.
A total of 5,596 people have been evacuated since the operation began on Monday with many being taken away on buses, French ministries said.
But charities claimed many young refugees were left without safe haven after a fire ravaged the makeshift site, cutting short the registration process for camp dwellers.
The minors required registration to access the shipping containers used to accommodate them in the heart of the camp, which itself was encircled by flames.
Save The Children said it was a "recipe for disaster" for the children left outside, many of whom fled or were exposed to the risk of people smugglers.
Spokeswoman Dorothy Sang, who is in the camp, said: "What happened yesterday put children in a serious amount of danger.
"Yesterday afternoon we saw fires rage through the camp and as children ran out, they ran out to find the registration process had been closed for a couple of hours, so there was nowhere for them to register to go and stay safe.
"Not only this but the containers were full, so you had this situation where children were running away from fire, couldn't register and the containers were full - so there was literally nowhere for children to go."
She said the streets that lead to the camp were lined with at least 60 youngsters, but other estimates had put the numbers a lot higher.
A handful of them were allowed to stay in a warehouse, but some were turned away, she added.
"This is a recipe for disaster in terms of child protection, because there have always been people who want to exploit the vulnerable in the Jungle camp - and now never have they been more vulnerable," she said.
Charity Help Refugees added in a post on Thursday: "This morning, at least 100 children were waiting in the minors' line to be processed at the registration centre. The centre was closed, and no officials present."
Firefighters fought to tackle a series of blazes blamed by officials on disgruntled refugees and migrants.
The prefect of the Pas-de-Calais region, Fabienne Buccio, said on Wednesday: "The camp is completely empty. There are no more migrants in the camp. Our mission has been fulfilled."
A total of 234 minors had been resettled to the UK since October 17, the French ministries of housing and the interior said.
Pascal Brice, head of the Office for Refugees and Stateless People, said everybody leaving the squalid camp had been registered at the processing centre on the edge of the site.
Despite this, campaigners said on Thursday that official estimates of the amount of people processed were lower than the total said to live in the camp, fuelling concerns that thousands could be left in the area.
Mr Brice told reporters on Wednesday afternoon: "The operation will be over tonight because all the people who were leaving the Jungle are now welcomed in France, in good conditions in accommodation centres.
"It is a matter of satisfaction for the French administration because all those people now are in centres all around France and the Jungle is over."
A spokeswoman for the local prefecture said the demolition would be sped up on Thursday with larger machinery moving in.
Help Refugees estimated that about 300 children were turned away when the registration centre closed.
Several large fires started tearing through caravans, tents and shelters in the centre of the camp a little before midday on Wednesday, the third day of the operation to clear it.
Four migrants have been arrested in connection with the fires, said Patrick Visser-Bourdon, the Calais police commissioner in charge of the operation, dismissing suggestions that British activists were responsible.
