Images surfaced on Sunday of Messi appearing to ignore instructions from Sarabia in the drinks break at Balaidos, with Setien looking on perplexed in the background.
"There are always controversies, like in life," Setien said in a press conference on Monday. "Everyone has their way of seeing things.
"Sometimes there are differences of opinion. I wasn't an easy player either in my day. You have a vision of your things.
"What you have to do is convince everyone that they have to defend the common idea. The communication is good. These are one-off questions and I don't give them importance."
Pressed on the incident involving Messi and Sarabia, Setien said: "Nothing happened. It was an indication and that's all. What else do you want me to say?"
Luis Suarez scored twice for Barca in Vigo, but Setien's side were pegged back by a Iago Aspas free-kick two minutes from time.
Afterwards, the Uruguayan was asked about the team's poor form away from home and responded that it was down to the coaches to find a solution.
"We all have to cede a part of ourselves," Setien said on Monday. "Including the footballers, for the good of the team.
"But I have a clear conscience. I'm doing all that is in my hands."
Barca are now two points behind Real Madrid in LaLiga with six rounds remaining and cannot afford to drop more points at home to Atletico Madrid on Tuesday.
"Winning has become a tremendously decisive question," Setien said. "Because anything can happen, but the matches are reducing and the margin of error is smaller."