The Potters trailed by two goals following an own-goal from captain Ryan Shawcross and a first-half effort from Luis Suarez before Peter Crouch and Charlie Adam, both formerly of the Reds, drew the home side level by the break.
In the 51st minute, Steven Gerrard restored Liverpool's lead when Raheem Sterling had been brought down by Marc Wilson prior to another Suarez goal which preceded Jon Walters late reply for Stoke and Daniel Sturridge's even later strike.
Hughes felt that the decision by referee Anthony Taylor to penalise Wilson was harsh and believed it had a massive effect on the outcome of the contest.
"Soft, easy - any adjective you like really," said the Potters manager.
"When players go down in the box the referee is going to have difficult decisions, we all know that, but I don't know whether that penalty would've been given at the other end.
"The reaction of the player himself, he immediately looks towards the referee, is a give-away and the fact there are about 3,000 Liverpool fans behind that goal as well reacting to it means unfortunately the referee has bought it and it's a poor decision.
"There was a hint of handball (by Sterling) and he has been given the benefit of the doubt.
"It was a difficult day in terms of what went against us but I thought we showed real determination to keep on going because that augurs well for big games coming up."
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