Dion Charles was given a second yellow card by referee Tom Nield after an incident with keeper Jay Lynch in the 68th minute, followed quickly by a straight red card for manager Ian Evatt.
Nield had been involved in a controversial incident in his previous game at Bolton when he mistakenly sent Charles off for an offence committed by Elias Kachunga.
Evatt’s dismissal meant that under new EFL rules he was unable to come to the post-match press conference to explain the situation.
Atherton deputised, telling the local press: “In terms of Dion, what I saw live, he was running behind the keeper, came alongside him and the keeper actually stuck his leg out and tripped him up.
“When the ref blew the whistle I’d expected it to be our free kick but obviously whatever he saw was different to what we saw on the bench, so unfortunately for Dion it was a second yellow.”
Wanderers have no route for appeal on Charles’s yellow card, meaning he will definitely miss the weekend’s visit of Wigan Athletic.
“In terms of yellow card you can’t get that rescinded and as far as I know the rules have not changed, so we expect to be the same. It is disappointing given the circumstances it happened,” he added.
Evatt’s exit was even more controversial, given it came as a result of new directives to officials on the “mis-use of technology” in the dugout.
Referee Neild was called over by fourth official Martin Coy, who reported the Bolton boss for having commented on the replay he had just watched of Charles’s second yellow.
Atheron said: “Based on the same incident the gaffer merely said he’d seen it back, he wasn’t making any reference in terms of abusive language he just said: ‘I have seen it back and you have got it wrong. The keeper tripped Dion up.’ And, apparently, just referring to having seen it back, that is a red card.”
The two incidents masked a fine first half show in which Victor Adeboyejo grabbed a hat-trick, taking him to four goals this season.
Asked if it was the best Bolton performance since he came to the club, Atherton added: “Apart from the Plymouth final – that was some game – it was a great start from the lads. I am made up for Victor. All the strikers have been working hard to add goals to the team and it is very pleasing for him to get a hat-trick.
“The goals mirrored each other, all came from crosses, and he finished it well. We got in a strong position off the back of it.
“We knew Fleetwood wouldn’t give up, it isn’t in their DNA, second half we started sloppy and allowed them to build up some momentum and then obviously the game changed with the sending off.”
Wanderers have now won their first four games in league and cup and join Peterborough United and Stevenage on maximum points so far.
Wiganer Atherton could now be tasked with patrolling the technical area on Saturday if Evatt’s ban is upheld.
“It is where I am from but at the end of the day I am here to win games for Bolton,” he said.
“It has been a very pleasing start. It is only a start, though, and there is a tough game at the weekend but we go into it on the back of three wins, which is great.”