The Dragons led by 12 points in the second half at home last Saturday but bled two tries and coughed up victory when inexperienced Souths half Jamie Humphreys slotted a field goal.
Flanagan privately apologised to Ilias for telling a reporter he was "smarter" than to ask for the coach's opinion on the form of his own halfback after he failed to ice the game.
Flanagan would not divulge the content of that apology but felt everyone had contributed to the 25-24 loss that leaves the Saints winless this season.
"(The apology) is my business but we definitely speak to all of our players and Lachie's just part of a team that didn't win. We'll move forward," Flanagan said.
"It wasn't Lachie's fault. Everyone contributed to the loss, the coaching staff and everything.Â
"We've just got to work harder and make sure if we're in front by 12 points, we get home, we nail it."
Playing only his second NRL game back from a long-term leg injury, Ilias sat down for an honest conversation with the Dragons' senior players after the game.
"You've got to be able to talk to each other as men. We're not kids. We're trying to win games of footy," said co-captain Clint Gutherson.
"It's high intensity, you've got to be able to make decisions under pressure.
"It's always the halves that get pointed at, it is their job, but we're all in it together. It's a team sport."
On the same day the first sod was turned at the site of the Dragons' Wollongong high-performance centre, Flanagan said he had turned over a new leaf ahead of the round-four clash with Melbourne.
The premiership-winning coach admitted his post-match comments, which included promises of a brutal bye week, had been made in the heat of the moment.
"That was probably more out of frustration from myself. This week has been planned for a long period of time and we're not going to change it too much," he said.
"My frustration is over, I need to prepare well for the team.
"We've reviewed our game. In the NRL, if you drag your feet for too long, you won't get the job done."
The Dragons should be training on their new high-performance centre at the University of Wollongong by March next year.
The centre, propped up with $13.6 million in Federal funding, will feature two training fields, a gym, treatment and meeting rooms and facilities for both NRL and NRLW players.
The Dragons will continue to take some training sessions to their home stadium in Kogarah but the centre is tipped to help the joint venture unify.
"Over the last 25 years, the connection between the clubs, it hasn't been strained but it has been hard," Flanagan said.
"Now we're under one roof. I've seen it work so many times before, how it brings a club together."
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