The squad's Mark Winterbottom/Steven Richards and Will Davison/Steve Owen entries had their chances of a race win in the Sandown 500 disappear due to a pitstop fumble and a strategy error respectively.
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Co-driver Steve Owen likened the incident to Red Bull Racing's ‘multi21' scandal from this year's Malaysian Formula 1 Grand Prix.
Edwards, who has led FPR for the last eight years without a single championship or Bathurst 1000 success, said post-race that he was unaware of such an agreement.
The bungle has clearly put further strain on the relationship between the team and Davison, who remains unsigned for 2014.
FPR's offer to Davison for next season is known to include a significantly reduced driving fee, triggering speculation that he could go elsewhere.
Making matters worse, the Sandown 500 unfolded in front of Ford president Bob Graziano, who is yet to commit backing to FPR beyond the end of the season.
In a question and answer statement distributed by FPR to selected media, Edwards downplayed the team's errors.
“I think any team that came away from the weekend with a qualifying race win, pole position and a spot on the podium at a tough event like the Sandown 500 would be happy and while we are happy, we know we should've done a better job overall,” he said.
“It is easy for outside observers to assume we've make the wrong call in the heat of battle or based off what someone says on TV, but if Frosty hadn't had his wheel nut issue we would've had two cars in the top four and probably a much tighter battle for the lead.
“If that was the case nobody would've thought twice about our strategy.
“Aside from the double-stack, which is a common occurrence in our category, Will's chances were hurt by his technical issues so we can hypothesise all day what might've happened, much like Frosty's slow pit stop, but the fact is without those issues it would've been a very different race.
“Those things happened, nobody is immune, and the team that had the least issues on the day won. It's as simple as that really.”
The statement, which also heavily criticised media coverage of the team's weekend, stressed that the culture within FPR is not toxic.
“The mood is a positive one as everyone is confident and believes in what they are doing,” said Edwards.
“Mark and Will have outscored every other driver in the field since Austin way back in mid-May. It proves that despite some reports we haven't had a ‘disastrous' weekend for quite a while.
“In fact, it is a tremendous feat in year one of Car of the Future and validates what we are doing.
“We have a lot of passion and drive within our business and work very hard on culture,” he added.
“Outsiders can have their view but everyone working with the team supports each other through the typical highs and lows of motorsport.
“There can only be one winner each race so having a strong group that supports each other no matter what provides a very motivating atmosphere.”