The Blues coach accused his team of not being hard enough, and of being taught a lesson in work rate and sticking to a gameplan by the visiting team.
He also described the performances of small forwards Chris Yarran and Eddie Betts as "horrible", and challenged Marc Murphy to rise above the close attention from taggers, after he was well beaten by Ryan Crowley.
"I don't think we were hard at all," Malthouse said.
"I've got a lot of admiration for Fremantle.
"The envy of my squad is the fact that they work hard, they work together, they work longer, they're highly disciplined, they don't panic and they finish well.
"They did all of those things tonight, and we did all the reverse of that."
Malthouse said the clearance statistics – 41-35 in Fremantle's favour – were flattering, because the Dockers were "clinical" in their exits from congestion, while Carlton was "grubby".
"There was no stage during the game, except probably that first goal, that I thought we did anything near enough to work with one another," he said.
"It was a very disappointing game."
Betts and Yarran managed just seven and 12 disposals respectively, with neither kicking a goal.
Malthouse was particularly hard on soon-to-be free agent Betts, whose contract negotiations with the club are dragging on longer than expected.
"His consistency at the moment is well down," the veteran coach said.
"We know his best, and Eddie is far from his best.
"But ... I can name 10 other players that had absolute stinkers tonight."
Murphy had only 13 disposals – four kicks and nine handballs – to be the biggest under-performer in a badly-beaten midfield.
He was unable to break free of Crowley, but Malthouse did not accept that as an excuse.
"Top quality players set an agenda to absorb the tag," Malthouse said.
"This is a learning curve for Marc, there's no question about that, and we spoke about it after the game.
"The top quality midfielders over the last decade or so get tagged, and what differentiates you between being a good ordinary footballer and a very good footballer is your ability to learn the lessons from the last tagger, and take them into next week and say, 'Righto, this is what I've got to do.'"
Carlton subbed Andrew Carrazzo from the game early in the second quarter, with Malthouse saying he had suffered a "badly bruised" calf.
If Port Adelaide beats Adelaide on Sunday the Blues will be two games outside the top eight, but they have a chance to make up ground next week against the 15th-placed Western Bulldogs.
