The midfielder was not in Mourinho's 18-man squad for the comprehensive 3-0 victory over Basel at Old Trafford on Tuesday, despite being fully fit.
Instead Mourinho opted for Paul Pogba and Nemanja Matic in midfield with Marouane Fellaini and Michael Carrick on the substitutes' bench, as United made a winning return to Europe’s top competition.
"No reasons to be out," Mourinho told reporters after being asked about Herrera's absence.
"We are playing only with two midfield players, with Matic and Pogba, which are playing really well and without reason to change.
"The only match that we decide to play with three [against Stoke City] he played.
"[Against Basel] we went back to two again and I had on the bench Carrick and Fellaini, which were also important players in the last season.
"We have a group of players and the players must be ready to play and not to play. Ashley Young was not on the bench in the last match and here he started the match and he played for 90 minutes.
"The next match you can have another surprise of some player that 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."
However, Herrera, who started the 2-2 draw with Stoke last week, could return at home to Everton on Sunday with Pogba likely to be ruled out with a hamstring injury.
The France international was set to have a scan on Wednesday to determine the severity of the problem he sustained in the first half against the Swiss champions.