Zlatan Ibrahimovic scored a hat-trick at Old Trafford as United beat their Ligue 1 opponents 3-0 to take control of their Europa League last-32 tie.
But Mourinho was unhappy by his side's poor first half, adding they were fortunate to reach half-time in front.
Ibrahimovic's deflected free-kick had given them the lead but only after a sloppy backpass by Eric Bailly presented Romain Hamouma with the game's first opportunity inside three minutes.
Despite not registering their first shot until the 30th minute, St Etienne had 11 attempts before the break, the most by an opponent at Old Trafford in the first half since Athletic Bilbao had 13 in March 2013.
"I had the feeling immediately in the dressing room," Mourinho said. "Too noisy, too funny, too relaxed.
"My assistants had the feeling in the warm-up with some of the guys not really focused on getting the right adrenaline in their bodies.
"The game started and the first thing we did was a backpass to a striker to be face-to-face with Sergio [Romero].
"A lack of concentration and when you don't have it, it's difficult to recover so the first half was hard and even myself on the touchline I felt that was difficult, the communication.
"I needed half-time so we were lucky, yes, to be winning at half-time 1-0. The second half was a different story and a different result."
Put to him that the attitude might be down to the fact it was the Europa League rather than the Champions League, Mourinho said: "I know Champions League is the competition everyone wants to play, everyone wants to win, I know that.
"But we don't play Champions League, we play Europa League.
"I think in the first half, it was too relaxed. Then, St Etienne were in the game with the right attitude and intensity, and they created problems.
"We don't play Champions League, so if that is the case I would prefer to play in the Europa League than be at home watching TV. So I think with the players it is the same."
Mourinho did stress the second half was "a different story" and said of the match overall: "To score three goals and not concede in the first leg at home, it's always a good result - it is not over, but it is a good result."
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Manchester United player Anthony Martial has answered Jose Mourinho's questions
Zlatan Ibrahimovic is a goalscorer
The Swedish striker is making a habit of these kinds of performances. If he hadn't scored against St Etienne, he would have taken a lot of stick because the ball breaks down on him more than it should. But he scored a hat-trick. And you can't ask for much more from your centre forward.
That's 23 for the season for the 35-year-old. It's an incredible tally for a player in his first season at a new club and in a new country. He deserves a lot of credit.
Jose Mourinho's organisation is paying off
It wasn't United's best defensive display. And Mourinho won't he happy that they allowed St Etienne to have 10 shots in the first half alone. But that's five clean sheets in a row for United.
It's an impressive run, especially because Mourinho has had to chop and change his back line.
Anthony Martial has bounced back
He hasn't been given a easy ride by Mourinho. But if his last two games are anything to go by, he is getting back to his best.
It wasn't a great United performance. But Martial was direct and dangerous and was unlucky not to get himself a goal.
He was still getting instructions from Mourinho for most of the game - about his decisions and positioning. But he is firmly back in the manager's plans.
Rashford can change a game
The knock-on effect of Martial's return to form is that Marcus Rashford has dropped out of the team. But he proved against St Etienne that he still has a big part to play, even if it is from the bench.
He came on at 1-0 and 20 minutes later it was three and the tie was as good as over. It owed a lot to the injection of energy and pace that Rashford introduced.
Blackburn has become a big game for Luke Shaw
Luke Shaw hasn't been in the squad for four consecutive matches, despite being fit again after a groin injury.
The suggestion is that he will start against Blackburn at Ewood Park in the FA Cup fifth round on Sunday. It is becoming clear that his opportunities between now and the end of the season will be limited, unless he can make an impression on Mourinho.
Blackburn is a chance to do that. If not, you have to fear for his future at Old Trafford.
JOSE MOURINHO UNHAPPY WITH MANCHESTER UNITED ATTITUDE AFTER SAINT-ETIENNE WIN
Manchester United manager Jose Mourinho slammed his side's attitude following their 3-0 victory over AS Saint-Etienne in the UEFA Europa League last 32 at Old Trafford on Thursday.
Zlatan Ibrahimovic netted a hat-trick to ensure United will take a comfortable lead to the Stade Geoffroy-Guichard for the second leg next week.
But Mourinho was not happy with his side's approach, especially in the first half, per PA Sport (via ESPN FC):
I am [happy with the result], especially because in the first half, we played so bad, and we managed to finish it winning 1-0 when we don't deserve. It was down to lack of concentration.
I had the feeling immediately in the dressing room—too noisy, too funny, too relaxed. Then my assistants had the feeling in the warm-up, with some of the guys not really focused on the getting the right adrenaline in their bodies.
The United boss added: "I am not happy with it. At half-time, the result could be 1-1. I always think we have to play every game with the same attitude."