I not only read the article, I read 15 other versions, ranging from the Guardian, Washington Post, the original AP news most places are reporting, and Der Spiegel's international translation. I commented elsewhere on the other matters you mentioned. I was also stationed there from Sept 2008 until Dec 2009 in Tikrit working in a Division level job with oversight of detainee processes.
The people who tried to surrender then fled capture again before ground troops could arrive. Look at the actual source. The underrepresented civilian casualties are a product of soldiers on the scene not knowing which were combatants or which were innocents in many cases. Not all, but many.
For the period of time there was a sovereign run Coalition government, we would be responsible for the actions of the Iraqi police and military while they rebuilt. But sovereign control of the country had been handed back to Iraq in 2004-2005, and we're talking many of the events in the source leaked documents occuring into 2010, when America has been "withdrawn" (despite still having over 50,000 troops there). There's got to be a cutting off point for liability. Japan took years to get a government running, like you said, but once set up, they took responsibility. Claiming Iraq is a distinct case from Japan is not sufficient. We still have troops in Japan. Japan has a known history for having an unrealistic criminal confession rate of about 95% due to police "coercion" for people to "confess." Are we liable for those acts since we helped set up a country with that kind of cultural practice? Of course not.