Madrid-based tabloid AS reported that Messi was upset at being substituted and had reacted badly towards his manager, but the Argentine has denied any wrongdoing.
"I didn't mean to make any gesture when Martino took me off. Nobody likes to be out, but we must accept it because it is the best for our team," he wrote on his official Facebook account.
"What I will not accept is that certain media tell lies about any situation that happens around me."
Barcelona beat Real Sociedad 4-1 in tonight's La Liga match to extend their unbeaten start to the season.