Both Messi and Villa featured in the Blaugrana's 2-0 victory over Granada on Saturday, with television replays showing the Argentina international berating his teammate after the collapse of an attacking move.
Nevertheless, the 25-year-old sought to play down rumours of a bust-up, and explained that it was in the heat of the moment, with the relationship between the two still positive.
"People shouldn't look for a problem where there isn't one. We've got a spectacular squad. These things are part of football, with the tension of wanting to score to make everything easier and win," Messi told the club's official TV channel.
"It happens in training, and in matches as well. I haven't got any problems with El Guaje [Villa's nickname], quite the opposite.
"These things show the character of the team, to want to win and keep on playing well. We get heated because we want the best, and the tension makes you react like that."
Nevertheless, Messi - who has six league goals already this season - insists that his side have started the season well, but must be wary of further challenges.
"We have to carry on this way, but keep in mind that there is a long way to go. But it's good to start like this and not drop points at the beginning, something that always happened in the last few years," he explained.
Tito Vilanova's side travel to Sevilla for their next La Liga fixture.