Sabella surprisingly started with a 5-3-2 in Argentina's unconvincing 2-1 win over Bosnia-Herzegovina in their FIFA World Cup opener.
He switched to their usual 4-3-3 at half-time and got better results as Argentina and Messi looked more dangerous.
Messi said he was unsure why Sabella initially opted for a five-man defence, but Sabella was unfazed by the Barcelona superstar's comments.
"Messi has said many times that he likes to play in a 4-3-3 system, with (Angel) di Maria getting involved in attacking movements," Sabella said.
"So, I repeat, he didn't say anything new, and he said what he said with all respect, so we don't have any problems. It did not bother me, and the morale of the squad is excellent.
"Every day you have two players in press conferences, you can ask them, and the one that says which player goes is me. I could send Messi, but I didn't.
"Here we live in freedom, and with total security with our professional or human performances. In our group, staff and players all have a great relationship."
Sabella warned his team to respect Iran, who they face in Group F on Saturday, despite being expected to win comfortably.
He said there were no easy games at the World Cup.
"We have to be very focused, and be very humble, from the beginning until the 90th minute," Sabella said.
"We don't have easy opponents, they don't exist. It is a World Cup game, and we can't underestimate anybody.
"This is not part of a speech. For me, it is a life attitude, and is the life attitude that a football team need to have. Play 100 per cent from the first minute until the last, and respecting absolutely every rival."
