Adel Taarabt wastefully chipped over for the visitors when presented with a good chance just before the interval and was unable to convert further opportunities after Charlie Adam's goal, while Potters goalkeeper Asmir Begovic did well to keep out an Esteban Granero effort.
"We've had this conversation too many times after games unfortunately," Hughes said.
"We played well as the away side - I thought it was a decent away performance.
"We restricted Stoke to very few chances. In general play I thought we were the dominant team in terms of how we wanted to get the ball down and play.
"But the key at the moment is that we have to take chances when they present themselves.
"We created good opportunities, but unfortunately didn't take them."
Hughes was keen to defend Taarabt, rating the midfielder's overall performance as "really effective".