North End captain John Mousinho scored the only goal of the game in first-half stoppage time.
It came from a deep corner from Jack King and the skipper found space to head across goal and through the legs of goalkeeper Scott Flinders, who four minutes earlier had produced a superb save to keep out Nicky Wroe's penalty.
After a fifth home loss in a row, Hughes said: "It just didn't go for us did it? Yes it was disappointing in the way we conceded the goal.
"Scotty made a great save from the penalty, then we give away a corner and they score form it - very disappointing.
"It would be nice if we were beaten by something good, some well-worked goal. We beat ourselves, it's the fundamental things and you have to make sure you are hard to break down and don't give things to the opposition."