United has progressed to the Europa League final four but only just, winning 2-1 on the night and 3-2 on aggregate against Belgian side Anderlecht.
The United manager also offered Luke Shaw fresh hope in his battle to salvage his Old Trafford career after praising the England left back's willingness to play through cramp during 30 minutes of extra-time against Anderlecht.
"I was not disappointed with Zlatan, I was disappointed with the team", Mourinho said at his prematch news conference ahead of Thursday's second leg against Anderlecht.
Pogba was the next player to miss from a golden chance, volleying over with an terrible attempt after Mkhitaryan's corner fell into his path six yards out, while Ibrahimovic lashed a shot wide after great work from Michael Carrick.
Regarding Marcus Rashford, Mourinho stated that, "even without scoring goals, even with being since September without a goal in the Premier League, was always a player I trusted, I played, I supported because he was always coming in my direction, in the direction I want from a player".
"You speak about his qualities and they are fantastic".
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Mkhitaryan struck again early on but United were given a scare, with Anderlecht captain Sofiane Hanni bringing the tie level, before Rashford capped a man-of-the-match display with the goal that secured a 2-1 extra-time triumph.
"It doesn't matter if he doesn't score - he is fantastic in his effort and attitude".
"The game was easy to kill", he said.
"You cannot do miracles, so miracles I don't expect but you have to do everything to accelerate the process. with a special spirit you can (come back) sooner than expected".
Mourinho gave his honest opinion on Anthony Martial when he said, "Do I think Anthony is a player with great potential?"
He added: "For Zlatan (Ibrahimovic) it would be fantastic to play the final in Stockholm, in his country".
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"A lot of people will say things about me but I just keep my head down and work hard".
The striker burst onto the scene at Old Trafford in February 2016 with two Europa League goals against FC Midtjylland on his senior debut for the Red Devils.
"I don't know whether the game should be played behind closed doors or somewhere else, but it would be very risky for us to play with the same supporters [as in the first leg]", he said.
"We lost players in the January market, we didn't bring in anyone, we lost players in global week, so we need everyone that can and Wayne can".
With the team currently marooned outside the top four of the Premier League, it is thought victory in the Europa League now looks the most likely route to Champions League qualification next season. "He can help us".
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