Martinez conceded his team were beaten by the better side, with the Latics lacking sufficient strength in depth to cope with a run of four games in 11 days.
"It was very unfair to play against the league leaders in a period like that," he said.
"We didn't have the legs or the reaction and you have to congratulate Manchester United.
"They had the luxury of making changes and Van Persie and Hernandez looked brighter and sharper. In the end it was a mismatch."