Stoke dominated for long periods at Britannia Stadium and held a deserved two-goal lead thanks to goals in each half from Victor Moses and Mame Biram Diouf.
But high-flying West Ham hit back, as first Enner Valencia turned in Stewart Downing's cross on the hour, before roles were reversed when the Ecuadorian centred for the Englishman to smash home a 73rd-minute equaliser.
Diouf had a great chance to restore Stoke' two-goal lead moments before Downing's leveller and Hughes, while fulsome in his praise of Stoke's overall performance, rued their profligacy in front of goal.
"I thought we were excellent from start to finish really," said the Welshman.
"We didn't play particularly well in the first half against Southampton on Wednesday [in their 3-2 League Cup defeat] but second half we were excellent we just carried on in the same vein today.
"In terms of performance, that is arguably one of our most creative and dynamic performances this season so I am delighted with the manner of that performance.
"But we obviously need to convert more chances than we did today because we were by far the superior team today and in terms of quality and creativity.
"All in all, I can't criticise the guys too readily because I thought, as an overall performance, it was excellent, but we are scratching our heads somewhat, failing to understand how we didn't take maximum points."
Hughes was less complimentary of referee Chris Foy's performance, as he felt Stoke should have been awarded a free-kick for a foul by Alex Song in the build to West Ham's first goal, which was also their first shot on target.
Hughes added: "We are disappointed with their first goal obviously, a poor challenge from Song, he dived in two-footed, two feet off the ground.
"Thankfully Mame Biram Diouf jumped out of the way but the game should have been stopped there and then. It was a poor challenge, a dangerous challenge.
"That's a poor decision from the referee, he needs to do better than that."
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