Vincent Kompany's close-range strike had cancelled out Antonio Valencia's stunning opener before Amr Zaki scored a contentious penalty to earn Steve Bruce's men maximum points.
Hughes felt City lacked the craft and guile to unlock north-west rivals Wigan and was disappointed to come away empty-handed.
He said: "For all our possession in the second half our tempo and momentum was not at a high enough level to ask more questions of Wigan. Once they were camped out in their own half, they were going to protect what they had and it was difficult for us to break them down.
"We got into decent situations without having that final pass or that degree of guile to be able to create really clear-cut chances. In the end, we did not test the keeper enough in that second half."