Herrera, 28, made his first Premier League start of the season in Saturday’s 2-2 draw at Stoke alongside Paul Pogba and Nemanja Matic.
But the Spain international was dropped from the squad as Manchester United beat Basel 3-0 in their Champions League Group A opener.
And Mourinho admits his decision was a tactical one as he favoured two in midfield and picked Marouane Fellaini and Michael Carrick ahead of him on the bench.
“No reasons to be out,” Mourinho said after the game.
“We are playing only with two midfield players, with Matic and Pogba, who are playing really well and without reason to change.
“The only match we decided to play with three [Herrera] played, today we went back to two again.
“And I had on the bench [Michael] Carrick and [Marouane] Fellaini, which were also important players last season.
“We have a group of players who must be ready to play and not to play.
“Ashley Young was not on the bench in the last match and today he started the match and played 90 minutes.
“And the next match you can have another surprise of some player you think is going to play and is not going to play.
“It’s the squad we have, I have to use the players and that’s the life in clubs with squads of quality.”