The 21-year-old has been struggling to secure regular first-team action under Mourinho and has not featured in the Premier League since October 2016.
He played the full 90 minutes in a 4-0 FA Cup win over Wigan last month, but has not been included in a matchday squad since.
Nevertheless, Mourinho is adamant he does not have any issues with the England international.
“He has to work and wait,” Mourinho was quoted as saying by Manchester Evening News.
“But Saturday I wanted one defender on the bench and the defender on the bench is somebody who can play more than one position.
“And [Matteo] Darmian can play left-back, right-back and would be an emergency central defender for us, so my choice was Darmian.
“The only thing I can say is that Luke is working well. I do not have any problem and he is working well. He is fighting hard, there is no problem with him.”