In the end, it was a bittersweet night for Manchester United. They are through to the semi-finals, courtesy of another outstanding addition for Marcus Rashford’s growing portfolio, but the victory came at a heavy cost bearing in mind the sight of Zlatan Ibrahimovic limping away with a jarring knee injury just before the tie moved into extra-time.

Ibrahimovic’s knee had bent to a point where there will inevitably be concerns about whether he is able to take any further part in the competition. He will undergo a scan to assess the damage and if United’s worst fears are confirmed, it threatens to be a considerable loss, even if Rashford’s end-of-season form indicates he is ready to fill the void.

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At one point Rashford, thrust into the central role after Ibrahimovic’s departure, could be seen clipping in an exquisite cross with a rabona, delivering the ball from behind his standing foot, and Paul Pogba’s overhead kick was threatening to register one of the great all-time Old Trafford goals before striking one of the players in Anderlecht’s purple.

Equally, Rashford was culpable during that long period after the hour mark when José Mourinho, once again, must have been pained by the profligacy of his players. Yet the teenager was hardly alone there. Between them Rashford, Ibrahimovic and Pogba missed more chances than they will probably wish to remember.

Ibrahimovic, indeed, has rarely looked so maladroit, putting in one of his least distinguished performances in United’s colours before that moment, late on, when he landed awkwardly after an aerial challenge and immediately signalled he was hurt. The Swede did at least manage to walk off but it did not look promising and the layoff may be a long one. He has just over a month before the Europa League final, should United get there, at the Friends Arena, Stockholm, the stadium where they are putting up a statue in his honour.

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As if that was not galling enough for United, this was also a night when they lost another of their centre-halves to injury. Mourinho is already without Chris Smalling and Phil Jones, with neither player expected back before mid-May, and Marcos Rojo was in considerable pain when he was taken off on a stretcher midway through the first half.

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Rojo had twisted a knee going for a tackle and having received some lengthy treatment, tried to continue before it became obvious in the next challenge that he was in no state to carry on. He, too, will need a scan and, worryingly for United, there were the tell-tale signs of what can often happen when players suffer knee ligament damage – a short, deceptive period when the initial pain wears off, an attempt to run it off and then the realisation that it is a worse injury than suspected.

Rojo’s injury meant Daley Blind taking over in the position where he played for long spells last season. Mourinho has made it clear he does not trust Blind in the same way Louis van Gaal did last season but the United manager did not have any other specialist centre-backs available and perhaps it was inevitable in these circumstances, with Sergio Romero in goal and Luke Shaw getting a rare start, that at times the home team seemed unusually vulnerable in defence.

Nine minutes after the substitution, Alexandru Chipciu’s cross was turned away by Blind but without enough distance to avert the danger. Youri Tieleman’s shot skimmed off Antonio Valencia and when the deflection took the ball over Romero to connect with the crossbar the rebound dropped between Blind and two opponents. Lukasz Teodorczyk could not rearrange his feet quickly enough to take advantage but the captain, Sofiane Hanni, walloped in his shot to level the tie.

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Anderlecht finished the first half as the more threatening side whereas early on Mourinho must have liked what he saw. Pogba’s pass to Rashford in the build-up to the opening goal, 10 minutes in, was a particular joy, beautifully weighted over 40 yards. Rashford’s first attempt to find Henrikh Mkhitaryan came back off the nearest defender but he picked him out the second time. Mkhitaryan took aim with his right foot and fired a low drive past Rubén Martínez.

The oddity at 1-1 was that it was not until midway through the second half that United seemed to remember they were the home side. It was an onslaught for the remainder of the match but Rashford took the ball too wide after going round Rubén, Ibrahimovic squandered two clear opportunities, the first from six yards out, and Pogba somehow volleyed over from even closer.

The game had ticked into its 107th minute when, finally, Rashford made the home team’s superiority count. His clever turn took him away from two defenders in one movement, creating the opportunity to shoot and his left-foot drive won a tie that finished with Mourinho marching pointedly towards the Anderlecht fans and applauding their support. “Shame on you” they had been singing at the early-leavers in Old Trafford’s crowd – and United’s manager was keen to applaud them.