Both players were subbed with the Red Devils two goals down and staring another defeat in the face, which may well have cost Mourinho his job at Old Trafford.
Replacements Marouane Fellaini and Alexis Sanchez helped inspire United to all three points in Saturday's 3-2 win, however, and Mourinho concedes that certain players may be struggling to cope with the pressure.
"Maybe it was my wrong decision to play Marcus Rashford and Scott McTominay," he told reporters. "They were not ready for this level of pressure that the manhunting is bringing. The boys woke up on Saturday and they didn't know if I was going to be at the game or not.
"I think they thought in the morning, 'Is he going to be there? Or is he not going to be there?' - because the manhunting influences people and it's not easy.
"For big boys like me it's no problem. But for younger people I think 'problem' - and I think in the first half they clearly showed that."
McTominay has featured in four Premier League games for United this season, while Rashford has been used five times.