The pair squared up during victory over Granada.
Sport says Messi was furious with Villa for taking a shot instead of passing to him: "Give it to me first!"
He then gestured to make the point he was in the clear.
Villa was having none of it and reminded Messi what had happened earlier in the first-half: "I couldn't see you, I couldn't control the ball. In the first-half I was clear and YOU didn't give it."
Messi has since insisted there's no problem between the pair.