Rashford, a 27-year-old player, came on at halftime but was taken off 33 minutes later as Barcelona beat Vissel Kobe 3-1.
In a post-match press conference, Flick said that Rashford was behind his new teammates in terms of training and acclimation.
He added that the coaching staff wanted to prioritize Rashford's health and well-being.
Flick praised the team's overall performance, noting that the first 30 minutes were excellent and the second half was also strong.
He also complimented Vissel Kobe on their tactics and ability to press Barcelona, saying it was a clear and interesting approach.