Colback looked to have snatched victory for the Magpies with a 74th-minute strike just three minutes after escaping a second yellow card - he had earlier been cautioned for a foul on Marc Muniesa - for a late challenge on Victor Moses.
The Potters hit back in the final minute of normal time when substitute Peter Crouch levelled to claim a 1-1 draw but Hughes, who was sent to the stands in the corresponding fixture last season after Glenn Whelan and Marc Wilson were dismissed in a 5-1 drubbing, was far from placated.
He said: "The disappointment, as you would imagine, is the fact that the referee wasn't brave enough to make the right decision at a key moment in the game.
"Given the yellow cards that were dished out, not only to ourselves, but to Newcastle as well and given the nature of the offences that caused him to give yellow cards, for him not to give a yellow card to the lad Colback when it was clearly a second yellow...
"We are not here advocating we want players sent off, but the referee needs to be strong and make the right decision there, and unfortunately he didn't.
"The lad is allowed to stay on the pitch and, lo and behold, he goes and scores the goal that possibly might have stopped us taking anything out of the game.
"If the referee had been strong and made the right decision, they would have been down to 10 and I think we would have won the game.
"As it's panned out, we have thankfully shown great determination and haven't allowed that decision or the conceding of the goal to affect our determination to get something out of the game, and we have gone up the other end, a great ball by Geoff Cameron and a fantastic header."