Nope. Even Messi wasn't looking for a penalty, he knew he'd been bettered.
Don't know how you can read Messi's mind but I think he was frustrated because penalty hasn't been awarded after Nesta kicked him.
And I wouldn't exactly say that Nesta bettered Messi after the latter mashed Milan's defense along with Nesta to set up Pedro. Or earned that FK on Nesta again from which Villa scored.
Nesta is good but let's not go crazy.
Except he clearly makes contact with the ball before the player, making it a fantastic tackle, which isn't a penalty in any game in any league.