Molina was called for catcher's interference on a swing by Braun, which followed some back-and-forth between the two players when the batter questioned a second strike call.
"Just because he gets mad at you, you can't call that a strike, man," Braun said to home-plate umpire John Bacon, referring to the Cardinals catcher, according to MLB.com's Adam McCalvy.
Molina appeared to hurt his wrist when it was struck by Braun's bat, causing Shildt to check on his player. The manager said he heard something from the Brewers that angered him, and he proceeded to walk toward the opposition and stare into their dugout.
No punches were thrown, as Brewers infielder and former Cardinal Jedd Gyorko helped de-escalate the situation.
Shildt seemed to question postgame whether Braun hit Molina with his swing on purpose.
"I want to make sure this is clear: There is no allegation against Ryan Braun, necessarily," Shildt said. "It just didn't look good."
He added: "There was a look in the dugout, there was something said, and at that point, all bets are off."
The Brewers and Cardinals play a doubleheader Wednesday and meet five more times from Sept. 24 to 27.