Hansi Flick protested there was a clear foul in the build up to Girona's winning goal, but said he didn't want to use it as an excuse after Barcelona fell to a shock 2-1 defeat at Montilivi on Monday.
Fran Beltrán struck in the 86th-minute after Thomas Lemar had cancelled out Pau Cubarsí's opener, although Barça felt Claudio Echeverri had fouled Jules Koundé in the build up to the goal.
The defeat saw Barça slip to second in LaLiga, two points behind new leaders Real Madrid.
"I don't want to speak about that," Flick said when asked if he thought Beltrán's strike should have been disallowed. "Everyone saw the situation before the second goal, but Girona deserved [to win]. We defend very bad, especially in transition, we were too open, our midfield was not in the right position.
"[Of course the foul] was clear, but it's like that. For me, I would maybe speak more about that if we played good, but we did not play good.
"It looks like an excuse, complaining. I don't want that. We have to play better. We have to come back on this level."
The decision came just days after Barça sent a formal complaint to the Spanish Football Federation [RFEF] and the Refereeing Committee [CTA] about what they perceive to be inconsistencies in the standards of officiating, prompted by Cubarsí's disallowed goal against Atlético Madrid las tweek.
However, Flick refused to be too critical of the referee here, even joking that his players had been just as bad.
"No complaining, no excuses," he insisted when pressed on the match officials. "They make their job. Sometimes it's not a good job, but they are on the same level that we played, so it's maybe not a good level."
Barcelona manager Hansi Flick has a heated conversation with the referee during their match with Girona. Getty Images
Defeat to Girona compounded a miserable week for Barça after they were hammered 4-0 by Atlético in the first leg of their Copa del Rey semifinal on Thursday.
They had taken the lead at Montilivi, Cubarsí heading them in front early in the second half after Lamine Yamal had missed a penalty just before the break.
However, Girona improved after falling behind in what was an open, compelling game, with Lemar levelling almost immediately after Cubarsí's opener and January signing Beltrán completing the turnaround late on.
"We are not in a good moment," Flick conceded. "I will give the team two days off now. It's important they rest.
"The players are really tired. Maybe with more control, less errors, it's a different game today. In the first half we had some chances, also the penalty, but it happens.
"It could be tiredness, but we have to have the hunger to win the games. After losing to Atlético, it was important to win today. We didn't get this.
"Everyone is disappointed. We will fight. We have time to come back now in the next two weeks with no midweek games.
"We will train good and come back for Sunday [against Levante at Spotify Camp Nou]. Now we have to fight and attack the first place in the table."
