The Catalan giants managed to secure victory thanks to goals from Antoine Greizmann and Sergi Roberto in the first half.
The Barcelona were on the receiving end of some rough tackles, and Setien was displeased that some of those challenges went unpunished.
"At full time they had made 29 fouls, but we have ended up with one more yellow card then them," he said in an interview with Marca.
"We have made 12 fouls and received three, I think this is wrong."
"I would like to know the referee's reason for this."
Setien also decided against shaking hands with Getafe manager Jose Bordalas, but he opted against explaining why after the game.
"I want to talk about what happened on the pitch, that is where football is played."
"We were nervous at the start, and Getafe made it very difficult for us with their press."