In particular, he had failed to take into account two earlier investigations into prison violence in 2009 - before Serco took over - and in 2014.
Mr Wilson said the investigation's findings were based on unreliable, anonymous allegations, which Serco had not had a chance to respond to.
The company was seeking access to the chief inspector's interview notes and the identities of some the witnesses, saying this would allow it to provide more context to alleged incidents.
Mr Wilson said Serco did not want to "pen the draft" or avoid criticism contained in the report. It had already accepted many of its recommendations, and simply wanted natural justice to take place.
In his submission, Mr Heron said the investigation was primarily about safety, and not about targeting Serco.
To illustrate his argument, he pointed to videos published on YouTube of "fight clubs" within the prison.
"There's only one word that describes it, it is sickening," he told the court.
"That is not a criticism of anyone, but what it does tell you is this is not about Serco. It is about safe custody."
He rejected claims that natural justice had not been served, saying the inspector had been "overly cautious" because he knew he was dealing with a multinational corporation that was facing serious allegations and potential damage to its reputation.
Mr Heron said Serco was over-reaching by trying to have the report revised and seeking access to witness statements and identities.
He said even in the case of the royal commission of inquiry into the Mt Erebus air tragedy in Antarctica in 1979, affected people were not able to get access to the sort of material Serco was seeking, and that inquiry involved the death of 257 people.
Mr Heron said Serco's main concern appeared to be about the tone and language of the investigation, not the findings, which were generally accepted by the company.