Setien rested the likes of Lionel Messi, Sergio Busquets and Gerard Pique for Wednesday's visit to the Segunda B club, who took a surprise lead after nine minutes against LaLiga's leaders.
An incredible upset appeared on the cards until Antoine Griezmann equalised in the 72nd minute and then netted the winner in the fourth minute of stoppage time.
Fati, 17, burst onto the scene with goals against Osasuna and Valencia earlier in the season and scored the winner at Inter in the Champions League last month, but contributed little to the 2-1 victory in Ibiza.
Despite his lack of influence on the contest, Fati will be provided with more chances to prove himself by Setien.
"The first thing we are doing is seeing the players in different positions," Setien told reporters.
"[Fati] has a lot of talent. We will see how he progresses. He will get more starting time as long as he keeps developing."
Setien was far from satisfied with Barca's performance, adding: "I did not like the team. I would have preferred things another way.
"But in a stadium like this, it is harder. They were aggressive and intense in defence. It has not been easy.
"I would have loved for us to have been more precise and to have played better. But from here we will take away conclusions for the future.
"It is when you do things badly that you can improve."