The Magpie stars were told their time was up at the club following the club's post-season reviews on Monday.
All three made valuable contributions in Collingwood's 2010 and 2011 premiership and Grand Final campaigns.
"I don't think with these guys, no disrespect to them either, that it wasn't a massive surprise," Pendlebury told reporters ahead of the AFLPA MVP awards on Tuesday night.
"We've got young guys that have stepped up already. So next year it's not like we'll have to fill three players' spots that have played every game."
Didak, Jolly and Krakouer all struggled with injury and inconsistent form during 2013, managing just 23 games between them.
Collingwood crashed out of the finals with a 20-point loss to Port Adelaide last Saturday night.
Pendlebury said the club was aware of where it stood in the AFL pecking order.
"On the weekend we probably showed that we're just a middle of the rung side," he said.
"We've just got to find a way to get better. I'm not sure what the magic formula is – it's usually hard work and once pre-season rolls around again, we've got to dig deep and go up a few extra levels because this year we weren't good enough."
Collingwood underwent a significant culture change in the 2013 season as the club implemented the renowned 'Leading Teams' program at the instigation of senior coach Nathan Buckley.
Pendlebury admitted there had been some obstacles along the way.
"It's always challenging," he said.
"But there's a perception out there that it's 'Bucks' versus the rest and it's completely untrue."
Twitter: @AFL_BenGuthrie
