Wolves fans vented their frustration during the game, although McCarthy defended his stance.
However, the Premier League have now got involved and want to know McCarthy's version of events.
A statement issued by the Premier League on Wednesday afternoon read: "The Premier League Board have written to Wolverhampton Wanderers to request their observations in relation to the team fielded in their League fixture against Manchester United.
"Once the observations are received the Board will decide whether any further action is warranted."
Although the Premier League's powers are wide-ranging, and include a points deduction in the worst-case scenario, it seems highly unlikely Wolves will receive anything worse than a rap over the knuckles.
Other than midfielder George Friend, who nearly gave Wolves a shock lead, all McCarthy's starting XI had featured for the first-team this season, with six full internationals also involved.
And the team was arguably not as weak as the one Sir Alex Ferguson selected at Hull on the final day of last season, 10 days before the Champions League final.
The Premier League did not intervene on that occasion and would have looked slightly foolish if they had done so after United won at the KC Stadium.
McCarthy would also presumably point out he was balancing the demands of a congested fixture programme with a number of niggling injuries, which left him to make what he admitted was likely to prove a noteworthy decision.
"The injuries tipped the balance," said the former Republic of Ireland boss.
"I don't have a policy and I am not worried about repercussions from the Premier League.
"I said I would play my best team and that was the fittest, strongest team I could pick."
Disgruntled Wolves fans chanted "We want our money back", "Where is our first team?" and "£42 to watch the reserves" as they expressed their frustration.
"I understand the reaction of the fans and I knew these questions would be asked," McCarthy added.
"But my decisions will be judged on whether we are still in the Premier League."
Even if they do not penalise Wolves with a fine, the Premier League will want to be seen to have highlighted the situation in an effort to ensure the integrity of their competition is not brought into question later in the season.
Mick McCarthy to last the season at Wolves. Click here to bet.