The Latics boss said that the real challenge for Wigan this season is Premier League survival.
"I don't see it as a setback. It's a fantastic competition, but for us winning the Cup is staying in the Premier League and our Cup final is the day we pass 40 points," Martinez said.
"I feel we are stronger now than we were before the Swindon game because I have seen nine players who can help the team."
Wigan are currently 19th in the League with 15 points from 20 games.