Tuesday's eventual game-winning run scored after Cubs outfielder Tony Campana was ruled safe stealing second by umpire Bill Welke. Cardinals second baseman Tyler Greene immediately began arguing with Welke as Matheny made his way on the field and was eventually ejected.
Replays showed that Campana never touched the base and, instead, grabbed Greene's shoe.
Cubs right fielder David DeJesus scored the game's first run on another questionable call in the first after he slid to the right of the plate and reached for it while trying to avoid Cardinals catcher Yadier Molina. DeJesus was called safe by home-plate umpire Chris Conroy and Matheny came out to argue.
Once again, replays showed DeJesus didn't touch home plate.
"There's nothing you can do. It's a judgment call," Matheny said of the calls Wednesday. "I'll give it to them that both of them were close, but both of them worked against us and both of them really hurt us."
Matheny said he thought the crew working the three-game series between the Cardinals and Cubs was one of the better ones in the league, calling Welke a "good umpire" and describing Conroy as a "very good up-and-coming umpire." Matheny said, for the most part, he has no issues with umpiring throughout the league.
"I do believe there's been more accountability now than there's ever been in the game," Matheny said. "It's as good as it's ever been, in my opinion."
Tuesday's calls brought conversation of instant replay Wednesday, which Matheny said he's an advocate of -- to an extent. He likes what Major League Baseball has done with home run and fair and foul calls, but said he doesn't want to see baseball "computer-run."
"For the game's sake, I don't mind having the human element. I think that's part of it," said Matheny, a former catcher. "There's also an art to that human element when you start getting down to calling balls and strikes. For a guy who made a living trying to make a borderline pitch look good, taking away that is taking away part of my livelihood. That's all part of the game and understanding the human element and trying to manipulate it when you can."
When asked about the possibility of expanding instant replay to plays at the plate, Matheny said, "Where do you draw the line? Because Campana's ended up costing us the game. I just don't know where it would end."