Stallings twice turned to fans and said, "At least we didn't pay our kids $100,000," according to multiple reporters in the area.
Following the game, Stallings was asked about the exchange.
"Somebody said something bad about my players. I'm just going to stick up for my players," Stallings said. "Probably said the wrong thing, but I'm not going to let people talk crap about my players.
"We're down, the game's over with, you don't need to insult kids who are out there trying to fight hard and do their best. So like I said, I probably should have chosen some different words, but I'm not going to let people take shots at our players."
Stallings' comments allude to Louisville's involvement in the FBI investigation into college basketball. Federal documents allege that Adidas funneled $100,000 to an unnamed player -- later identified as five-star recruit Brian Bowen -- to sign with Louisville, at the request of a Cardinals coach.
Head coach Rick Pitino and athletic director Tom Jurich were eventually fired as a result of the investigation.
Interim Louisville head coach David Padgett said he wasn't aware of the incident involving Stallings until a question was asked in his news conference but he knows his team has been -- and most likely will be throughout the season -- heckled on the road. At Purdue, Boilermakers fan came to the game wearing FBI shirts.
"We've just got to ignore that," Padgett said. "Our players at Purdue, they didn't let it bother them, so it's not anything we're going to talk about or pay attention to."
Information from The Associated Press was used in this report.