The withdrawal came after the final team sheets were submitted, which raised the ire of Scott, however Clarkson said there was no deliberate dishonesty intended.
"We were trying to get him to the line but he'd been ill on and off in the previous 24 hours so he did the warm-up and coughed up blood," Clarkson said on Friday.
"Our doctors have got the status that says when a player does that, don't run the risk of playing him in a game. It was a bit of a hiccup for us. We certainly would have liked to have at least one ruckman playing."
Clarkson said he had moved on from the game and had no concerns with Scott's comments.
"That's past and gone. We're focussing on the Bombers this week and we went into the game with no ruckman. We felt like that was a real hurdle we were unable to overcome over the course of the four quarters," he said.
"I'm not sure whether it cost us the game or not but it certainly didn't help us get a victory over the Kangaroos."
Clarkson admitted the team was missing injured tall Simon Taylor.
"We'd prefer to have two [ruckman] and we've got one this week. Hopefully he (Renouf) will be able to make a pretty solid contribution for us against [David] Hille and [Paddy] Ryder."
He said the focus on Hawthorn's violent clashes with Essendon during the week was not an issue for the club.
During the week a Channel Ten advertisement for the game highlighted the history of violent matches between the sides, but Clarkson said it was the AFL's job to monitor how games were promoted, not Hawthorn's.
The AFL publicly chastised the network for the advertisement but Clarkson said: "We don't take particular interest, to be fair.
"We've got 22 guys to prepare for the way we want to play the game and we've got more pressing things to worry about than the way the game's being portrayed.
"We've got AFL administrators and media to control the way the game's being portrayed. We'll focus on getting out there and playing footy."
