But his behaviour in his clash with Thomas angered Di Matteo, who felt it led to the red card that gave Arsenal the upper hand in their third-round tie.
With the game goalless, Thomas, a former Arsenal trainee, clattered Wilshere with a tackle but the two were seen to exchange angry words before Thomas lashed out.
Di Matteo accepted that Thomas ultimately deserved his dismissal, but added: "I'm disappointed that Wilshere didn't accept his hand.
"He wanted to help him get up, actually. He's a fellow colleague. But, anyway, that's part of the game.
"I'm very proud of my players and my team. I'm not disappointed in my player. Thomas went to shake hands, Wilshere refused and Thomas reacted. There was an exchange of words and a reaction."
Wenger said Wilshere was injured in the initial challenge but could not shed any light on what followed.
"I could not hear anything from the touchline," he explained.
"Thomas has reacted, and in these cases you always need to control your nerves. Have you any excuses? I don't know - but Jack looked upset as well, he said he has been kicked."
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