Ankara accused the United States, a NATO ally, of "unacceptable" behavior for such an overt display of support for the Kurdish People's Protection Units (YPG).
"Wearing those YPG patches was unauthorized and inappropriate, and corrective action has been taken," Baghdad-based military spokesman Colonel Steve Warren told Pentagon reporters.
"We have communicated as much to our military partners and military allies in the region."
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The United States has more than 200 special operations troops in northern Syria, where they are advising the so-called Syrian Democratic Forces, the bulk of which is made of YPG fighters.
The commandos are supporting the local forces as they push toward Raqa, the Islamic State group's Syrian stronghold.
While it is not unusual for US special operations forces to wear the insignia of partner forces, Warren said in this case it was inappropriate to do so given the "political sensitivities" around the issue.
Ankara regards the YPG as a terror group, accusing it of carrying out attacks inside Turkey and being the Syrian branch of the Kurdistan Workers' Party (PKK) which has fought an insurgency against the Turkish state for over three decades.