Barca won 3-0 via goals from Ferran Torres, Dani Olmo (penalty) and Robert Lewandowski.
Flick said afterwards: "Yes, it's a great time. There are 10 games left, and we're three away from second place...
"The situation wasn't easy; it wasn't the best time to play. We paid the price for playing with (Dani) Olmo's injury, and I'm leaving with that bitter taste in my mouth."
On Olmo, he said: "He's injured, and with this schedule, you miss a lot of games in two weeks.
"I think we made the most of the situation we're in today. It wasn't the most appropriate day to play after the break. It wasn't opportune. But we've got three more points. The injury isn't bad, we don't know how long he'll be out, but two or three weeks... the price for these three points is very high.
"We have 10 games left in LaLiga, and the Girona game, the next one, is the most important. The players played optimally. We need Pedri, Dani, Gavi... Gavi had a fantastic game. The non-regulars also played well; it was a fantastic day.
"But it wasn't easy after the international matches. I spoke with Frenkie, Lewy... and we've managed very well. Everyone is focused. This is positive for the team."
On the calendar, Flick said: "I think we have to listen to the players, and the coaches. In the summer, there's the FIFA World Cup, the Nations League... the players go with their national teams... it's very hard. I don't think it's an optimal situation.
"That's my humble opinion. You can earn a lot of money, but it's not good for the players. You have to think about the players. The fans want to see a spectacle, but if we continue like this, we won't be able to maintain this level."