Hughes' charges were beaten by Jason Puncheon's 51st-minute strike, which came following a mistake by Oussama Assaidi, who presented the ball to the winger inside the penalty area after initially winning possession from Adrian Mariappa.
It was Stoke's third successive away defeat, and Hughes' side have not won away from the Britannia Stadium since their 1-0 win at West Ham in late August, their first away fixture of the season.
And former Wales boss Hughes could not hide his disappointment at the manner of the defeat.
"We needed to play better than we did to deserve to get anything out of the game," he said.
"It was a low-quality game from both sides. There wasn't much guile or creativity shown and I include ourselves in that.
"Unfortunately we didn't have enough in the final third to cause many problems of real note and that's where we are at the minute.
"We're okay at the back and through midfield but we find it difficult to create clear-cut openings and chances.
"I'm disappointed we weren't able to build a performance that was going to enable us to take the game away from Crystal Palace."
Goalkeeper Jack Butland made a number of stops in the final five minutes as Stoke were left exposed at the back, including an incredible triple save to deny Joel Ward, Puncheon and Stuart O'Keefe, and Hughes said his performance was a rare bright note.
"He did great today in fairness," he said.
"He was the outstanding one for us, but we had too many off the level we needed and we can't afford to carry that because it's too much for us."
