Spurs progressed to the semi-finals of the competition with a 3-1 victory but Mourinho felt that the midfielder was culpable for Stoke's equaliser after he lost possession of the ball.
Mourinho said: "For me a player that plays in that position is a player that has to link and create and not to create problems for his own team.
"In that situation, an objective counter-attack would probably end with a goal, and it ended with a counter-attack behind our defenders.
"We were unbalanced because when you are in possession you have full-backs out wide and another midfielder in a different line and they caught us in a counter-attack and they transformed the result of the game that was totally in our hands, so yes I am upset."
Gareth Bale scored the opening goal for Tottenham but Mourinho revealed that he requested to be substituted due to the possibility of a calf injury.
The Portuguese coach said: "Yeah, it was his decision.
"Something he felt in the last part of the first half and he didn't want to come out before the second half so he stayed. While he was walking to the dressing room he told me immediately that he couldn't come for the second half.
"Something I think with [his] calf. I'm not sure as at that time I just want to reorganise the team and make the change."