Gaudreau, 22, leads the Flames with 21 goals and 28 assists. His 49 points place him in a tie for 10th in NHL scoring. Monahan, 21, is second with 16 goals and 35 points in 51 games. Bouma, 25, has one goal in 17 games this season.
"It was very simple," said Flames coach Bob Hartley, who declined to comment on which team rule was broken. "We established team rules at the start of the season. We're a very proud hockey club. We have built what we believe to be a very strong culture and that goes for everyone.
"I know people say, 'It's the top two scorers.' It's not the players. It's not about the people involved. It's about the Calgary Flames. It was tough. It was tough because you can't get three better young men. They're proud of representing this community. They're easy to coach and everything, but when you make a mistake, we have to be accountable and we have to be fair to everyone."
Gaudreau represented Calgary at the 2016 Honda NHL All-Star Game alongside Flames captain Mark Giordano.
"It [stinks] that it happened and they know they made a mistake," Giordano said. "We're not looking at it as three guys or whoever is out. We've got to take our lumps as a team. Yeah, we learned from it as a team. I think you can't find three better guys. It was a mistake, and that's what we're looking at it as -- one mistake. We know and they know it won't happen again. We tried to play our hearts out for those guys. They'll come back and be stronger than ever.
"I think it's pretty clear, it's straightforward. There's rules. But again, you look at those three guys and as far as teammates is one thing, but as people you can't find better guys. It's a tough situation. They know they made a mistake. They've owned up to it. As a group, I think we're going to be better in the long run for it."
Gaudreau, Monahan and Bouma reportedly arrived late to Scotiabank Saddledome prior to practice Monday. Bouma left practice after 15 minutes with what Hartley said was an illness.
"They didn't rob a bank," Hartley said. "They made a mistake and tonight they paid for it and it's the last time we'll address it. They're great kids.
"It's nothing bad on them. Who didn't make mistakes when they were young? Everyone. We support those kids, we need them and they learn a very valuable lesson tonight."