The Austria international publicly showed his disapproval at being substituted in the 2-1 defeat at Hull on Saturday, moments after the Tigers' opening goal for which he was partially culpable.
"Paul is a winner and a great professional, and I have no problems with what happened," said the Latics boss.
"It was nothing out of the norm for me. There is nothing to forget because it was never an issue.
"He was obviously very disappointed because it was his man who scored from the corner. He wanted to put it right, and that is a natural reaction."
Scharner has also complained in the past at having to play at centre-back, where he spent much of last season, although Martinez has mostly employed him in midfield so far.
The Wigan manager welcomes the versatility the 29-year-old brings to his team.
"I think Paul is at that stage of his career that he understands the different positions really well and it's not a big problem for him at all," he told the Wigan Evening Post.
"He is a good aerial threat, especially at set-pieces, which is useful, and he gives us many options in front of goal.
"But he is responsible enough to play in any position that the team needs him to play in, and that is the most important thing."