Messi injured his left thigh at the 18 minute mark of their 4-1 La Liga win, pulling up sore after sprinting with the ball at his feet.
Barcelona has confirmed the Argentine star will undergo scans on Monday to determine the extent of the injury.
"We'll have to talk to Lionel (Messi) and see if he's worried because of this, his third injury of the season," Martino said.
"It's true that it didn't take long for him to overcome the first, but this is the third one and it could affect him mentally."
Martino was full of praise meanwhile for midfielder Cesc Fabregas' efforts to score a brace in the second half.
"Cesc Fabregas is such a complete footballer. He can do whatever he likes. He can assist, he can score, he can start plays, he can finish them off."
But despite the convincing win away from home, Martino insisted there was still room for improvement from the defending champions.
"We positioned in the pitch where Betis wanted us in the first 30 minutes," he said.
"We knew their defence would stay up and therefore that we were getting spaces at their back. But we didn't want to stay back that much.
"We did so because of their pressure and this didn't prevent us from creating chances. We managed to score twice even though they deserved to score as well. But at the start of the second half, similar to the first, Fabregas scored and finished off the game.
"The pitch wasn't easy for us to play on either. It was hard to get our combinations going we had to play smart football to overcome this. Betis deserved their goal."
