Opposition boss Antonio Conte smartly replaced Alonso minutes later, which he put down to a tactical alteration more than anything, and Chelsea went on to add two more goals to their tally in a 4-0 win.
Speaking after the match, Hughes told reporters: "The referee has made a call on Alonso. He could have been sent off and should have been in my view. Their manager agreed he was lucky because he took him off.
"Those are the moments you need to go for you. The referee allowed them to stop the game. Chelsea are very much a reflection of their manager in the way they manage the game."
Stoke have lost more Premier League games (14) and conceded more goals (42) against Chelsea than they have against any other side in the competition.