The 19-year-old was dropped to the substitutes bench for Manchester United’s 0-0 draw at Anfield against Liverpool.
Mourinho told reporters before kick-off on Saturday afternoon that Rashford’s absence from the starting line-up was due to an injury.
“Rashford was injured with the national team. We don’t have many options,” Mourinho said.
“I never complain about that. I was just mentioning it to you because the next question is maybe why is Rashford not playing.”
Journalists had been asking the Portuguese why centre-back Eric Bailly wasn’t in the squad.
The Ivorian was one of the three players to suffer an injury during the international break, with Rashford and Marouane Fellaini the other two. Fellaini may be out for a month after a knee injury with Belgium.
Striker Romelu Lukaku also looked less lethal than usual against Liverpool, perhaps due to having a knock himself while playing with Belgium.
However, some of United’s key players were fresh, including Rashford’s replacement in the side, Anthony Martial, who wasn’t in the France squad.
Rashford was fit enough to make the bench, and so it must have simply been a minor knock to keep him from playing the full game.
The Reds have more key games coming up after the draw against Liverpool, facing Benfica twice in October as well as Tottenham Hotspur at the end of the month and Chelsea on November 5.