McGugan was surprisingly not named amongst the substitutes at Turf Moor at the weekend, and it led to question marks over Carvalhal's decision to drop him.
Wednesday fell to a 3-1 defeat against the Clarets, but Carvalhal has explained his controversial selection choice - insisting that it was the right thing to do.
"We have a lot of players in midfielder and there are games where we want players who can run and fight," he told the BBC. "For example, against Burnley, Kieran Lee and Sam Hutchinson ran and fought a lot, so it's just an option.
"I have Alex [Lopez] and [Barry] Bannan on the bench, who can play inside also, so sometimes it's better to put them on the bench, as they offer a lot of solutions [due to their versatility]. On the bench sometimes you need players who can play in multiple positions."
McGugan was one of Wednesday's star players towards the back end of last season, and completed a permanent move to Hillsborough over the summer.
However, he has not played since the middle of August in any capacity, with Wednesday's depth in midfield areas in evidence.
The Owls have a number of different options in the centre of the pitch, after a busy summer, and Carvalhal has tinkered to find the perfect formula.
The Portuguese boss has named a number different starting line-ups this season, and it seems that his rotation policy is set to stay in place for the time being.