Rooney cleared over elbow
England striker Rooney caught McCarthy off the ball in an innocuous situation on the halfway line a few minutes into the game at the DW Stadium, which United won 4-0.
Referee Mark Clattenburg awarded a free-kick against United but did not caution Rooney.
Wigan manager Roberto Martinez was furious and said Rooney should have been sent off, while analysts and TV pundits lined up to condemn the action which has been replayed repeatedly on TV.
The FA said on Monday that Clattenberg confirmed that he had seen the incident and taken what he considered appropriate action, leaving the FA powerless to take any further action should they have wanted to as video evidence can only be used in incidents unseen by match officials.