The French government sent troops to Mali in mid-January at the request of a government struggling to thwart the advance of Islamist and foreign rebels.
Ham, leader of the U.S. Africa Command, said at Howard University in Washington that mistakes were made during a U.S.-Malian military training program. Capt. Amadou Sanogo, who led a military coup in early 2012, was trained by U.S. military forces.
"(This is) very worrisome for us," he was quoted by the Defense Department's news service as saying.
Mali lost control of northern regions of the country following the coup. Foreign and al-Qaida fighters have declared autonomy for the area.
French advocacy group International Federation for Human Rights stated this week it confirmed that Malian forces carried out summary executions and other abuses during their rebellion.
Souhayr Belhassen, president of the group, said the abuses led him to suspect the worst is yet to come in Mali.
"We didn't ... (train) that to the degree that we needed to, I think," said Ham. "I believe that we focused exclusively on tactical and technical (aspects). So we've learned from that."