Cloke, who won Collingwood's best-and-fairest last year and has been the main forward target this year, was rumoured during the week to be ill with glandular fever, a claim denied by the club.
But the 21-year-old struggled on Saturday night, garnering just six touches and four marks.
"I sometimes get very upset with the Bronx cheers for a bloke who was our best-and-fairest winner last year, Travis Cloke," he said. "Travis really was quite ill after last week's game.
"He recovered, otherwise he wouldn't play, but he's effectively carried our forward line – the big-man division – for most of the year.
"It's the kids that have come through and have given him some support. They weren't great today, but that's a learning curve for them, to be able to say they've played in finals football – now they've got a taste for it, hopefully they'll be better for it.
"But a lot's been left up to Travis for the whole year, and he wasn't well after the game, and we gave him a couple of days to recover. He trained well [on Friday].
"But that avenue dried up, and then it was left for two other young blokes, who just didn't see a lot of the footy."
Delivery into the forward line was also an issue, Malthouse said.
"There was congestion there, but when you win the football as often as we did – and not as often as St Kilda – I just thought that for people who can kick the football, we really did almost demand too much of players in the front half.
"When we started to use the football properly, we actually were able to get through it.
"We went inside 50 more often, but our entry wasn't our usual 'give our forwards a chance' entry.
"I thought we really did rush it, and I didn't think we used the ball well at all."
