Barca moved level on points with leaders Real Madrid, who face Celta Vigo in their game in hand on Sunday, courtesy of first-half goals from Antoine Griezmann and Sergi Roberto at Camp Nou on Saturday.
The Barca-linked Angel Rodriguez gave Getafe hope when he pulled one back in the second half, but the reigning La Liga champions were not to be denied all three points.
Head coach Setien felt referee Cuadra Fernandez should have come down harder on what he deemed to be spoiling tactics from Getafe.
Asked what he was saying to the fourth official, Setien said: “I was complaining because many times you risk going out from the back and when you are fouled you have to start over.
“That hurts the pace of the game. I think they have made 30 fouls against 12, and we had one more [yellow] card.
“I think the referee had to be more severe. Sometimes you have no luck.”
Setien was not interested in discussing why he did not shake hands with his opposite number Jose Bordalas.
“I want to talk about what happened on the pitch, that is where football is played.” he said.
“We were nervous at the start, and Getafe made it very difficult for us with their press.”
Barcelona’s disciplinary record this season is rated as 13th among the 20 sides in the Primera Division. They have seen 53 yellow cards and five red cards. Only Real Betis, Setien’s previous side, have been reduced in numbers more frequently.
Getafe, meanwhile, have the second-poorest disciplinary record in the league, with 77 cautions – a league-high figure – and a couple of red cards.
Barca’s next match arrives next Saturday when they face Eibar at Camp Nou. Three days later, they will play Napoli in Italy in the first leg of their Champions League last-16 encounter and will then travel to the Bernabeu for a Classico encounter against Real Madrid that promises to be vital to their championship hopes this season.