Barcelona took the lead early in the second half when Pau Cubarsi rose to head home, but Girona responded quickly and completed the turnaround in the 86th minute through Fran Beltran. Barca felt Claudio Echeverri had fouled Jules Kounde in the build-up, yet Flick chose not to dwell on the decision.
"I don't want to speak about that," Flick said. "Everyone saw the situation before the second goal, but Girona deserved to win. We defended very bad, especially in transition. We were too open and our midfield was not in the right position.
"Of course the foul was clear, but it's like that. If we had played good, maybe I speak more about it, but we did not play good."
The defeat left Barcelona second in La Liga, two points behind leaders Real Madrid, compounding a miserable week after their 4-0 Copa del Rey semi-final first-leg defeat to Atletico Madrid.
Before Cubarsi's opener, Lamine Yamal had missed a penalty just before half-time. Girona equalised almost immediately through Thomas Lemar, setting up a tense finale that Beltran ultimately decided.
Flick, whose club recently lodged a complaint with the Spanish Football Federation over refereeing standards following Cubarsí's disallowed goal against Atletico, again avoided direct criticism of officials.
"No complaining, no excuses," he insisted. "They make their job. Sometimes it's not a good job, but they are on the same level that we played, so maybe it's not a good level."
The German coach admitted fatigue may have played a part. "We are not in a good moment. The players are really tired. I will give them two days off now. It's important they rest.
"After losing to Atletico, it was important to win today. We didn't get this. Everyone is disappointed, but we will fight. We have time now with no midweek games. We will train good and attack the first place in the table."
Barcelona return to action next Sunday against Levante at Spotify Camp Nou, knowing their margin for error in the title race has all but disappeared.
Real Madrid head coach Alvaro Arbeloa has admitted he wants to "eliminate" Jose Mourinho and Benfica when the two sides meet in the UEFA Champions League play-off first leg at Estadio da Luz on Tuesday night.
Barcelona head coach Hansi Flick is expecting a strong reaction from his team when they face Girona in their La Liga clash at Estadi Montilivi on Monday.
Barcelona could be without Marcus Rashford for their upcoming derby against Girona after the forward sustained a knee injury in last weekend's La Liga win over Mallorca.
Frenkie de Jong expressed frustration after Barcelona suffered a 4-0 defeat to Atletico Madrid in the first leg of their Copa del Rey semi-final, a match marred by controversial officiating.
