The Barca boss felt that his team were on the wrong end of decisions made by Polish official Szymon Marciniak as they fell to a 4-3 defeat (7-6 on aggregate) in the second leg at the San Siro on Tuesday (06.05.25).
Flick told reporters: "I don’t want to talk too much about the referee, but every decision that was 50-50 went (Inter’s) way.
"I am disappointed, but not with my team. They tried everything. It’s the way it is. We are out, but next year we will try again to make the fans happy.
"It makes me sad ... My team did an excellent job. I don’t like talking about the referee ... I’ve told him what I think, but I’m not going to say it here what I’ve said."
The defeat ended Barca's hopes of winning the Treble but Flick has urged his team to channel their disappointment into this weekend's crucial El Clasico clash against Real Madrid - which could prove decisive in the La Liga title battle.
He said: "We’ll learn from this. It’s a progression. We want to keep learning. We don’t have much time to train now, but next weekend we are back. It’s normal to be disappointed.
"The team deserves the respect they have earned. We play to win, we want to win titles and we have La Liga, with a very difficult match. We have a few days to prepare for this match.
"Each player, when they get home, can look in the mirror and be proud of themselves. We’ll analyse the game calmly and see what we can do."