The duo have reportedly endured a difficult relationship since Luis Enrique returned to the club as coach for the 2014-15 season, although neither has commented publicly on the issue.
The argument between the two is said to have occurred when the players returned from their mid-season break, with Messi seeing red after being the victim of a heavy challenge in a training match.
However, Mathieu added that the issue was swiftly resolved, with the pair making peace later that day.
"It happened when we got back from our holidays," he told RMC. "Suddenly, Leo lost his temper after a foul that was not given in training. Things got tense and they exchanged some angry words.
"Luis Enrique then approached him in the dressing room afterwards to talk to him and that was the end of it.
"It happens at every club, but more is made of it because it is Barcelona. That's the problem."
Barca are one point behind Real Madrid at the top of La Liga, having played a game more.
