Tottenham signed the right-back for £15 million last month, a move that many felt was great value for Spurs given his form for Wolves in the last couple of seasons.
However, Doherty was one of a number of players Mourinho criticised after the lacklustre showing against Everton.
Matt was struggling to play the way he plays.
“I could also feel some of my players are not fit. Matt (Doherty) was struggling to play the way he plays, as an example.
“We also had other players who were I think a bit in trouble with the physical point of view, due to the very strange reasons for some and for some not even a pre-season.
“But congratulations to my dear friend Carlo (Ancelotti) and the Everton boys.”
Mourinho was also critical of the match officials, claiming that Everton got an advantage for the free-kick that led to Dominic Calvert-Lewin's winner.
“It’s not an excuse for the result or the defeat and not a good performance, but with so many officials on the line, to take a free-kick a minimum of five metres distance, I feel it’s incredible.
“As I was saying before the goal, I was already saying that to the referees. Five metres difference on the crossing situation makes a huge difference in the position of our back-line and in the direction of the cross."
Doherty and his teammates will be hoping to bounce back as Tottenham face Bulgarian side Lokomotiv Plovdiv in a Europa League second qualifying round clash on Thursday before an away game against Southampton on Sunday.
Doherty was preferred to Seamus Coleman, who he faced yesterday, at right-back for Stephen Kenny's first two games as Ireland boss.