Trump ordered the withdrawal of all 2,000 US troops in Syria in December after he said they had defeated Islamic State militants in Syria.
Footage obtained by AFP from the Free Burma Rangers, a Christian aid group run by a former USA special forces operative, showed hundreds of people still remained in the riverside camp.
The International Rescue Committee on Friday said as many as 12,000 people from Baghouz have arrived in one camp for non-combatants in northeast Syria over the past 48 hours, including some 6,000 people on Thursday alone.
This comes after hundreds of militants recently surrendered and evacuated from the village, alongside thousands of civilians, after USA -backed forces began their attacks on the town.
The latest wave of evacuations brings the final defeat of IS by the Kurdish-led Syrian Democratic Forces one step closer.
The Syrian Democratic Forces (SDF) have slowed their offensive on the jihadist enclave at Baghouz near the Iraqi border to allow many thousands of people to leave over the past few weeks. The fighters, with women and children, made up around 2,000 people who left the village during the day.
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The men, their faces covered, were divided into three groups - Syrians, Iraqis and those of other nationalities.
Around a tenth of the almost 58,000 people who have fled the last IS bastion since December were jihadists, according to the Syrian Observatory for Human Rights, a Britain-based war monitor. Hundreds of others jihadists surrendered, though it was not yet clear how many, the commander added.
The skeletal and dishevelled figures shuffling out of the smouldering ashes of the "caliphate" may look like a procession of zombies, but many appear to have their devotion intact. Engulfed in conservative black robes with a black face covers, they pointed their fingers at the sky and screamed: "Islamic State will stay, God is great, God is great, Islamic State will stay!"
"Almost everyone agrees, however, that the Islamic State will live on in some form or another to fight elsewhere-Libya, Europe, the Sinai Peninsula, the Sahel or even Syria", he wrote, claiming that this "half-assed and potentially permanent deployment that may not be capable of accomplishing anything at all".
Votel indicated major combat operations were expected to be completed soon against ISIS, but the US withdrawal of most of its roughly 2,000 troops in Syria ordered by President Donald Trump in December would not necessarily coincide with the caliphate's collapse.
The refugees are civilians who fled from areas in southeastern Syria that were formerly controlled by ISIS.
Syria's Kurds hold hundreds of foreigners accused of fighting for the terrorist group, along with their family members, but their home nations have been reluctant to take them back.