Manager Nigel Clough said he believed the deal was done, but Naylor's agent, ex-Stag Jake Speight, came up with an 11th hour deal for the former Portsmouth captain to join League One Wigan Athletic on a more lucrative three-year contract.
“It was frustrating to say the least and disappointing,” said Clough.
“Tom actually came in for his medical and we were at the stage where everything was agreed.
“But unbeknown to Tom and anyone else his agent was still negotiating with another club behind everybody's back, even when the deal had been agreed.
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“I think it's about different standards of your behaviour.
“When we thought Tom might be available, and we knew he was out of contract, we made contact with him. And personal circumstances gave us a chance.
“We thought at least his agent is an ex-Stags player as well. So he will hopefully keen on him coming here.
“We were very surprised when one of the first conversations David (Sharpe, CEO) had with him the agent said he didn't want him coming here.
“The first thing he asked was how much was he getting out of the deal and the second thing was that he didn't think this was right for Tom.”
Clough continued: “It's disappointing, not that it happened but how it happened and the behaviour.
“In sharp contrast we dealt with Danny Johnson's two agents. We told them what had happened and they were disappointed as it reflects badly on them.
“The majority of agents we deal with are good and honourable. They said their principle was they tell their players once you agree a deal that's it. There's no going back.
“I feel a bit sorry for Tom as he was happy, then all of a sudden, behind his back, he is presented with this bigger financial offer at the last minute and he had to explain.
“He was obviously a bit embarrassed by it but you can understand as he's got a baby on the way, and he's nearly 30 years old. He has to make these difficult decisions. But, as far as we were concerned, the deal was done.”
Naylor would have been in competition for a centre half spot.
“We have got Rawson, Hewitt and Perch who can play centre half,” said Clough.
“But Tom was going to be a big signing for us and one we were excited about.
“It was a heavy deal for us. He was going to be our highest paid player as you'd expect bringing in the captain from Portsmouth in League One. But we move on and go for someone else.”
Clough has other irons in the fire and has told Rollin Menayase he can leave if wants regular football.
“We have agreed with a young goalkeeper to come in on loan and we are also very close to agreeing with our first choice on loan as well and a young defender too,” he said.
“We may bring in one more too. We do have three players, Rollin Menayese, Corey O'Keeffe and Marek Stech all of whom are looking for fresh clubs at the moment with a year left on their contracts.
“So we are conscious that until at least one of them goes we will probably stick with what we've got after these signings.
“If there are people out there interested in Rollin we'll listen to offers. The club paid a small fee for him and he is still under contract another year.
“He wants to play and we can't guarantee him that place.
“We have had a few calls this week, one from another League Two club about Corey and one or two bits of interest about Marek. But there's nothing concrete at the moment.”