Also seething over comments from Magpies coach Nathan Buckley about an incident between Kangaroos forward Lindsay Thomas and opposition defender Ben Reid, which left Reid concussed, Scott said the loss had left him "bitterly disappointed".
He said the Kangaroos had won the midfield battle, amassing more clearances and going inside attacking 50 more often, but their inability to hit targets enabled the Magpies to rebound with devastating effect.
"It's as poorly as we've used the ball in 12 months," Scott said post-match.
"They scored a hell of a lot from our mistakes.
"You've got the classic 12-point play, which played out time and time again.
"It wasn't through lack of winning the ball or lack of winning clearances – our midfield performed well.
"We were just terrible with our ball use going forward and couldn't make them pay."
That his team was unable to creep in front left Scott feeling particularly flat.
"We were coming home with a wet sail at the end," he said.
"I'm adamant we ran out of time, because we were coming home OK, but the ball use in the third quarter in particular was just terrible.
"You don't beat good teams like Collingwood when you use the footy like that."
One of the victims of the poor ball use was star forward Drew Petrie, who booted just one goal from four marks and 13 disposals.
"He probably wanted to stop leading, the amount of times it was kicked over his head," Scott said.
"But that's not to take away from [his direct opponent] Nathan Brown, who I thought did a really good job on him."
The Kangaroos take on Geelong at Etihad Stadium next Sunday.