He said Cooper - who denied to the inquest hearing Bollinger say that - told him when the pair had a beer at the drinks put on at the SCG for his brother on November 27, 2014.
Jason Hughes lists eight principal grievances or concerns he has about the day his brother died.
They include the fact "the other 14 people on the field that day could be crucial witnesses ... what haven't the players and umpires been spoken to and interviewed?"
He also questioned why there was no match report, the "level of medical care and how long it took to get Phillip to hospital", and the number of "borderline" balls not called out by the umpires.
Greg Hughes said in his submission "those balls were not getting pulled up" and said video of the game showed his son indicating something was awry.
"The footage ... showed my son giving hand gestures to his team member Tom Cooper at the other end as if to say, 'What is going on?'"
Jason Hughes said he had viewed the video of the game and identified three bouncers during over 47, with only one being called by the umpires.
He said the video also revealed Bollinger spoke with both his brother and Cooper after the second last delivery of the 44th over.
Phillip Hughes' sister, Megan, said she was "shocked' by the amount of time that passed between being told her brother was going to St Vincent's Hospital and his actually being taken from the field.
Megan and her mother, Virginia, were at the game which the family had hoped would enhance Phillip's chances of getting back into the Australian side.
"We all knew, including Phillip, that this match could be the answer to our prayers, but in other words, it was just the opposite."
Megan said after being told Phillip was going to hospital "soon, soon", she remembered "time passing, a lot of time".
"I had no idea why we weren't straight on our way to hospital with Phillip.
"Then I saw Phillip was still on the field and hadn't left yet. At this point, I was shocked.
"I believe things were not dealt with in the manner they should have been.
"My brother deserved the best care and the best people around him doing their job.
"If there are mishaps that have happened we need to settle this and hopefully receive an end result that will help us progress through life without our dearly beloved son and brother."