Mr Erdogan said the sight of American flags in the convoy alongside YPG insignia had "seriously saddened" Turkey.
The YPG is the Syrian branch of the Kurdistan Workers' Party (PKK), who have waged an insurgency since 1984 inside Turkey that has left tens of thousands dead.
Mr Erdogan said he would bring up the issue with President Donald Trump during his planned visit to Washington on May 16 -- and called for the coordination between the US and YPG to "come to an end."
The US-YPG cooperation began under the Obama administration, and while Mr Trump said he would rethink the relationship when he took office, little has changed.
"This needs to be stopped right now," said Mr Erdogan. "Otherwise it will continue to be a bother in the region and for us."
"It will also bother us as two Nato countries and strategic partners," he said.
Turkey sent its troops into Syria in August 2016 in support of rebel fighters and as part of an offensive aimed at clearing out Isil and creating a buffer zone between itself and the Kurds.
The International Crisis Group (ICG) said in its latest report on the Syria crisis that the US had "a singular dilemma" on the future of its relationship with the YPG.
It said the YPG "is indispensable" to defeat Isil but there is also "no avoiding the fact" that the US is backing a force "led by PKK-trained cadres in Syria while the PKK itself continues an insurgency against a Nato ally."