Roberto Soldado's first-half penalty set Spurs on course for victory, with impressive Mousa Dembele and Aaron Lennon efforts adding gloss to a first home league win since sneaking past Hull on October 27.
This loss for Stoke was hardly the ideal response to the Boxing Day thrashing at Newcastle, but one which Hughes felt could have panned out differently had referee Kevin Friend ruled against Tottenahm defender Zeki Fryers and Michael Dawson in the first half.
"In the initial period we had a couple of decisions that we were disappointed with," the Stoke boss said.
"Obviously Jon Walters going through the middle, we felt he was impeded and there was a case for their lad to be sent off.
"Oussama Assaidi also went into the box and felt he was impeded as well. He went down and that could have been a penalty all before Spurs got their penalty, which was a little bit harsh but I can understand why it was given.
"You need those things to go for you in the early part of the game and if we had gone into the lead it would have given us real encouragement and who knows?
"But, if I am honest, in terms of the quality on show and the way Spurs played, we found it very difficult to get anywhere near them.
"They were a little bit sharper to each and every ball, half-a-yard quicker.
"They are a good team and they looked fully motivated, each and every one of the players wanted to get on the ball and affect the game and we found it difficult to get a foothold in the game ourselves, unfortunately.
"There are reasons behind that. We were missing players today which would have helped, but, overall, on occasions we did not help ourselves.
"We allowed situations when we had good possession to be given up too cheaply in poor areas for us, but good areas for Spurs and they were able to capitalise on it."