The LaLiga leaders lost 2-1 at Anoeta after La Real overcame Marcus Rashford's equaliser for Barca following Mikel Oyarzabal's opener through Goncalo Guedes' winner.
Flick said afterwards: "I'm not happy. I'm disappointed. We had many clear chances, and the result doesn't reflect what happened. But I liked how we played. We made mistakes in defense; we need to defend better.
"We were also unlucky in attack. We have to accept it. We must focus on the next match, which is very important. There are games every three days. Today we were unlucky.
"Our game has been good. We could have defended better on a couple of occasions, but overall I'm satisfied. We've played very well in the last two weeks and we need to keep it up; we can't focus on the referee. We'll concentrate on what we can change."
On Gil Manzano, Flick also stated: "I'm not disappointed with the referee. Everyone saw it. I won't waste energy on that. We're focused on ourselves. We should have scored more goals; we had chances.
"We're going home empty-handed. Before the match, I'd already read comments about the referee. I always speak highly of them. But Frenkie is right; he's calm. He's the captain. He's on the pitch, he wants to talk to him, and he can't. Sometimes I also want to talk to the fourth official, and I can't; you have to accept it.
"I don't know if there's a lack of communication with referees in Spain, but with Gil Manzano, there's definitely a lack of communication."