Alli was substituted in the 66th minute with scores locked at 1-1 at the time, before gesturing towards the bench in frustration upon his replacement, despite having played reasonably well.
The England international had tested Stoke keeper Andy Lonergan twice before being substituted, but Mourinho was upset with his role in Stoke’s equaliser from Jordan Thompson.
“A player in that position is a player that has to link and create and not to create problems for his own team,” Mourinho said.
Alli has barely played for Tottenham this season, managing only four Premier League appearances, among which is only one start.
The 24-year-old midfielder has been linked with a January move to Paris Saint Germain and the latest issue will make that more likely.
Speaking about Stoke’s equaliser, Mourinho elaborated: “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, who was replaced due to a calf injury, scored the opening goal, before second-half strikes from Ben Davies and Harry Kane sealed Spurs’ spot in the last four where they’ll face Championship club Brentford.
Manchester United also progressed on Wednesday, winning 2-0 at Everton, meaning they’ll face rivals Manchester City in the semis.