Jonny Howson netted in the 34th minute at the Britannia Stadium with a strike from outside the box as the Canaries took advantage of some sloppy play by their opponents.
The visitors had already hit the crossbar through Ryan Bennett and were good value for their lead but they survived a nervous moment after the break when Leroy Fer appeared to pull back Kenwyne Jones in the box, with no spot-kick being given.
Hughes, whose side are now 15th, also on seven points from six games, said: "We didn't see that coming because we have been really good. That is the disappointment and the mystery.
"I thought, heading into the game, we were in good shape.
"We said at the beginning of the year that on occasions this season there would be days where we don't get it right.
"But there is a minimum requirement for what you have to do in a game to affect it, and you need the vast majority of your players playing at that level, allowing you to compete.
"Unfortunately, we didn't have enough players at the right level. As a consequence we didn't make it too difficult for Norwich, and it was an easy result for them. From our point of view that is a galling thing."
On Fer's challenge on Jones, Hughes added: "It is a penalty, but we are not going to hide behind that missed decision.
"I think if we are honest, Norwich deserved to win today because we didn't do enough."