Wanderers travel to Millwall today to face Feeney with a patched-up back four that has looked shaky since McNaughton returned to his parent club Cardiff City at Christmas.
And in a frank admission to The Bolton News, Freedman said he regretted not “nailing down” both players before they had even turned out for the Whites.
“Looking back on my time so far, I’d try to buy one or two of the players before I’d taken them on loan.
“That’s a judgement you make and there are different details to each one but when someone comes into this building it’s because I want to keep them.
“It means I have looked at them, analysed their game, and they fit in with what I want from them.
“So if I’m honest, and in hindsight, I wish I’d nailed down a deal for both Liam and Kevin.”
Feeney made just three starts for Wanderers in a loan spell that started in October and proved an instant hit with supporters.
But his success prompted then-Millwall boss Steve Lomas to try to force a permanent deal through before the January window opened.
Freedman said at the time that the club “would not be bullied” into the purchase and would rather wait until the summer when the 26-year-old’s contract expires.
“Liam Feeney had a price on his head and I felt comfortable with it at the time,” Freedman reflected.
“We were getting him on loan and I thought we would be able to pay that in January. I was happy with that.
“But the whole thing broke down because they wanted the money after he’d played two games for us.
“It’s a shame because he’s a good player and I still look out for him.”
On McNaughton, Freedman revealed how he tried to sign the Scottish defender in the summer only to be told he wanted to play in the top flight with the Bluebirds.
When his chance failed to come under Malky Mackay, he was loaned out for a successful three-month spell that coincided with Wanderers’ most consistent form of the season.
A second loan spell was heavily mooted but Freedman’s chances disappeared when McNaughton managed to earn a regular spot under new Cardiff boss Ole Gunnar Solskjaer.
Wanderers may have missed out on other defensive targets as they waited for the 31-year-old to become available but Freedman laments the fact he could not have signed his fellow Scot at the start of the season.
“I’d had a conversation with Kevin’s agent in the summer and he had a testimonial coming up and wanted to sign a new contract with Cardiff to play in the Premier League,” he said.
“When he came to us, Malky (Mackay) said it was on condition that he was only being loaned and would be going back at some point.
“I did enquire to buy but he said ‘let’s just see how we go.’ “With the change in manager, things change, opinions change, and the chance had gone. But that’s how it has gone for us just recently, isn’t it?”