Ricardo Horta’s 72nd-minute strike was the difference at Molineux – and Nuno was left ruing his side’s missed chances.
The Wolves boss said in his post-match press conference that the story of the game was Braga had one chance and scored.
Patrick Cutrone, Ruben Neves and the returning Willy Boly all had chances to open the scoring, but Braga were the only team to hit the back of the net.
Nuno said: “We are all disappointed.
“It was a tough game, but I think we did enough.
“We did not perform perfectly, but we created many chances.
“Braga had one chance, were very organised, and they scored.
“That is the story of the game.
“The boys worked hard, but that is football.”
After the 5-2 defeat to Chelsea, Nuno brought Ryan Bennett and Willy Boly back into the starting XI for Jesus Vallejo and Romain Saiss.
But Wolves’ defence were cut open once again, with Horta sprinting in unmarked to score his fifth Europa League goal.
However, Nuno would not point the finger. When asked how much individual errors are costing Wolves, he answered: “Like you say, we analyse and see what is wrong with the team.
“The analysis of the mistake is on the process as a team and let’s work on that process as a team.”
Nuno’s opposite number Ricardo Sa Pinto classed the victory as an historic moment for Braga.
But Nuno says he and his side know they are not playing well as he looks for improvement and their first Premier League win of the season at Crystal Palace on Sunday.
He said: “We realise the situation that we are in and we face the reality that we are not playing well.
“We have to analyse and find solutions for the team to improve.
“Sometimes you look back and see where we are and this cycle of games is a challenge for us to improve.
“That is what I’m thinking – now we need solutions for Sunday’s game.”
But why does Nuno feel Wolves have found it so difficult in recent games?
“Because we have played against good teams,” he said. “Sometimes you don’t do everything that you can.
“One of the ideas that we can come strong on the games.
“I think we started well. But we must come strong on Sunday.
“We must react immediately, make decisions and try for solutions for the best of the team.
“We must grow out of this situation and improve. Go out and bounce back immediately.”