Goalkeeper Marcus Hahnemann was the only player retained from the starting XI at White Hart Lane, as McCarthy sought to give his first-choice players a rest ahead of their home match against Burnley at Molineux this Sunday.
But Moxey feels McCarthy was acting in the club's best interests, despite the 3-0 defeat.
"We have a squad system at the club and Mick picked what he thought was the best side for that match." he told Sky Sports News.
"In fact if George Friend had taken the chance he had early in the game then maybe we could have held on just like we did at Tottenham."
Moxey also said the club has no plans to refund the fans who travelled to Old Trafford, despite a chant of "Forty two quid to watch the reserves" being heard from the away supporters.
Moxey said: "We have no plans to refund the £42 that they were chanting, about although we do have an empathy with them.
"We are very disappointed that we lost the game, but we have a squad system."
"I don't think we are going to get any complaints from other teams.
"We have also had a large amount of injuries recently, Michael Kightly is out and we have lost Andy Keogh.
"It's an old saying but the season is a marathon not a sprint and Mick's job is to keep us in the Premier League."
Moxey also refused to rule out the possibility that McCarthy would make wholesale changes to his side at other points later during the current campaign.
"He might do, he said." "He has already done it once."
Wolves Evens, Draw 12/5, Burnley 14/5