The incident in early May stoked long-standing tensions between Afghans and foreign troops over civilian casualties.
Afghan officials have put the civilian death toll as high as 140 while an Afghan human rights watchdog put the total at 97, including at least two Taliban fighters.
But the US military says 20-35 civilians were among the 80-95 people killed, adding that most of them were Taliban fighters who used the civilians as human shields.
The Times report did not say how many civilian casualties may have been avoided if the correct procedures had been followed.
The Pentagon has not officially responded to the report.
General David Petraeus, the head of US Central Command which is the military headquarters overseeing US military operations across the Middle East and into Central and South Asia, ordered the investigation.
The Times, citing an unnamed senior military official, said the investigation had concluded that one US aircraft was cleared to attack Taliban fighters, but circled back and did not reconfirm the target before dropping bombs.
That, the report said, left open the possibility that the fighters had fled or civilians had entered the target area in the intervening few minutes.
A compound where fighters were massing for a possible counter-attack against US and Afghan troops was struck in violation of rules that required a more imminent threat to justify putting high-density village dwellings at risk, The Times said.
"In several instances where there was a legitimate threat, the choice of how to deal with that threat did not comply with the standing rules of engagement," the newspaper quoted its source as saying.
A second military official told the Reuters news agency that the mistakes appeared to be linked to the choice of weapons used in the operation rather than any violation of the rules themselves.
The official said the investigation was still being reviewed and it was possible Petraeus could ask for further work to be done before the report was finalised.