Erik ten Hag said Tyrell Malacia and Jadon Sancho were substituted for their lack of movement on the ball rather than their roles in Omonia Nicosia's opening goal.
Omonia took a surprising lead when Sancho's careless pass was met with an errant touch by Malacia, who was dispossessed midway through the Omonia half to spark a breakway that Karim Ansarifard finished in the 34th minute.
Malacia was withdrawn at half-time in the second game running, along with Sancho, for Luke Shaw and Marcus Rashford. Rashford scored United's equaliser and eventual winner in a dicey 3-2 victory.
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"It (the goal) was not what I was happy with, it was the movement with our ball," Ten Hag explained of his interval changes. "The width on the left side, for me, was no good first-half. The movement from behind the defending line.
"So I hoped with Luke and Marcus we get more effect from that and so in my opinion that happens."
Anthony Martial, another arrival off the bench put United 2-1 up before Rashford tapped in for 3-1, only for Nikolas Panayiotou to strike a minute later in the 84th minute.
United had a staggering 28 attempts at the Omonia goal but wasted umpteen opportunities on what should have been a more comfortable night.
Ten Hag agreed United were thrown by Omonia's goal and the Cypriot side's manager Neil Lennon felt half-time came at an ideal time for United.
"I would call it stay composed," Ten Hag added of United's reaction to trailing. "It can always happen, football is a game of mistakes. I agree with you, first 30 or 35 minutes, we played quite well, the only thing we didn't do was score a goal.
"When you score a goal you make your life easy, we didn't. Then we concede a goal and it was the worst 10 minutes from the game from us. After half-time, we dealt well with the setback."
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