Messi opened the scoring early in the game and later hit the winner in the 90th minute from the penalty spot after Unai Lopez had levelled for the promoted side.
However, the five-time Ballon d'Or winner was almost motionless after his goal sealed the three points for the Blaugrana in a difficult week which had seen the Catalans lose 4-0 to Paris Saint-Germain in the Champions League.
“I didn’t see whether he celebrated or not," Luis Enrique said after the game when asked about Messi's reaction. "And I’m not the person who has to answer that.”
It was another disappointing display from the champions against a side without a win since November in La Liga, but Luis Enrique said his team were better than they had played in Paris on Tuesday.
"Compared to the PSG game, I think we were better in everything," he said. "We were much better. It's obvious that we are not as fluid in terms of goalscoring chances, but we were better than we were in Paris - even if some people don't see it."
And the Asturian added that he has no complaints about his side's attitude.
"In terms of effort, teamwork, the distance the players covered, the intensity, their attitude was impeccable in Paris," he said. "I haven't seen a better attitude in the previous seasons.
"Clearly things aren't going for us and we are trying to change that."