Colback gave Newcastle the lead in the 74th minute when he drilled home from just inside the area.
However, the former Sunderland midfielder had appeared fortunate to escape a second yellow card for a foul on Victor Moses three minutes earlier.
There was a late twist in the tale as substitute Peter Crouch powered home a far-post header in the 90th minute to ensure a share of the spoils for Stoke.
Yet that did little to appease Hughes, who was quick to express his disappointment at referee Kevin Friend's decision not to dismiss Colback.
"The disappointment on the day is the lad that's scored the goal," Hughes told Sky Sports. "We feel, and I think most people in the ground watching on TV, would say that he shouldn't have been on the field of play.
"It's clearly a second yellow card, given how easily the referee was giving cards out earlier in the game, for him not to give a second yellow is a big oversight.
"It's a key moment in the game and those are the ones that frustrate as managers when the referees don't get those right."
Colback, to his credit, was quick to show honesty in agreeing with Hughes that he was lucky not be shown a red card.
"If I'd seen a second yellow, I couldn't have felt too aggrieved," Colback conceded. "I caught him [Moses] but you ride your luck sometimes."
