Mkhitaryan, who has been on the wrong side of Mourinho's "tough love" campaign before, struggled upon his arrival and was left out of many matches by the Portuguese tactician.
The 28-year-old will return to the United squad for Saturday's Premier League game against Brighton.
"Frustration starts in the first half, I was counting to my assistants: one two and three, then four and five, then Martial six, Fellaini seven, we go to half time 0-0 and put ourselves in this situation and in the second half it would be hard to have the same number of chances".
"I was not happy with his last performances", said Mourinho of a player who has scored twice in 16 games this season.
Mourinho will be hoping he can close the gap at the top this weekend when Brighton head north to face United.
When asked if he would prefer Manchester City's Pep Guardiola to be in charge, he added, "Manchester United, it's like Barcelona. I refuse that situation because we are a team in the first half we should be winning five or 6-0 and that was not Daley's fault for sure so we put ourselves in this position".
And former United captain Ferdinand criticised the display, particularly the second-half showing which followed a promising start from the visitors.
"The first half the attitude was good, the football was good, is really hard to blame just football, easy match to win and then you lose, great for them, they have a good chance to qualify". "It's as simple as that".
"For many weeks, the question was - why do they not play together?"
Germany playmaker Mario Gotze arrived back in Dortmund in 2016 after three seasons at Bayern Munich while Turkey midfielder Nuri Sahin had a season at Real Madrid and a loan spell with Liverpool before returning, initially on loan, after a two-year absence in 2014.