But as footage emerged of the rebels hurling insults and threats at the American special operators, US officials were forced to play down reports that the troops did not receive a warm welcome to the frontline.
Last month, Ankara launched an offensive into northern Syria dubbed "Euphrates Shield," ostensibly designed to cut a major IS group supply line but also to counter the advance of US-backed a Kurdish militia.
US forces are working alongside the Syrian Kurds of the YPG in the fight against the Islamic State, but Turkey regards the group as terrorists and allies of the PKK separatist group fighting within its own borders.
In Syria, Turkey prefers to work with Arab and Turkmen fighters such as those of the Free Syrian Army (FSA), which is opposed to Syrian leader Bashar al-Assad's regime but has also clashed with the Kurds in the past.
Pentagon spokesman Jeff Davis told reporters that US commandos, at Turkey's request, had joined the Turkish military and "vetted Syrian opposition forces" fighting the Islamic State group near Jarabulus and Al Rai.
But footage widely shared online by Syrian groups and experts appears to show US commandos in Al Rai insulted by FSA fighters, who call them "pigs" and "infidels" in Arabic, demanding they leave Syria.
A US defense official admitted there had been a "misunderstanding," but insisted the troops were still deployed and that the matter had been cleared up.
"There's been no violence, no one is hurt and we are still there," the official said. "I have no report of a hostile or violent action."
The special forces contingent includes several dozen troops, he added.
America's top general, Chairman of the Joint Chiefs of Staff General Joseph Dunford, met with his Turkish counterpart General Hulusi Akar on the sidelines of a NATO chiefs of staff meeting in Croatia on Friday to discuss the anti-IS group fight.
His assistant, Captain Gregory Hicks, said the generals met "to advance discussions on the way forward in the fight against ISIL, and recommitted to the close military-to-military and strategic relationship the US has with Turkey."
Meanwhile, in another incident underlining the four-way tensions between Kurds, Turks, Americans and Syrian Arabs on the battlefield, Kurdish YPG fighters again flew US flags near Syria's border with Turkey.
An AFP photographer saw the stars and stripes flying over a YPG base in Tal Abyad. The use of US flags is seen as a provocation by some in Turkey and the Pentagon repeated its request for them to be taken down.
"We would call on our partner forces not to fly the American flag on their own," Cook said. "I would imagine that that would be communicated if indeed that's taken place in this instance."
There was some good news for the coalition, however.
Cook said that senior Islamic State propagandist Wa'il Adil Hasan Salman al-Fayad, known as "Dr. Wa'il," was killed in a precision strike on September 7 near Raqa, the Syrian city that is the group's de facto capital.
