The hosts raced ahead as the fit-again Bojan Krkic marked his first Barclays Premier League start in eight months with a goal in the 13th minute, and Jonathan Walters then pounced on a Wes Morgan error to double the advantage seven minutes later.
But high-flying Leicester produced yet another stirring comeback to get something out of the game, with Riyad Mahrez converting a penalty after Marko Arnautovic was adjudged to have fouled Danny Drinkwater, before Jamie Vardy held off Erik Pieters to scuff in the leveller.
Hughes was angry no action was taken by referee Andre Marriner or his officials in the build-up to the Vardy goal when Morgan tangled with Walters at the other end of the pitch.
And the manager - whose side remain in the relegation zone and without a Premier League win this season - said after the game: "In the first half I think we were fine.
"At two goals to the good we were in decent shape, and we talked to them at half-time about not conceding and the importance of the next goal.
"Unfortunately we made a mistake - Marko got the wrong side of the guy (Drinkwater) who has made a run into the box.
"It looked like he caught his heel outside the box, but given the performance of the officials today, there was always the likelihood it was going to be given as a penalty.
"We shouldn't have allowed that situation to develop
Then for the second goal we maybe got a little bit distracted by, once again, the referee not really officiating as well as he should have done.
"Jonny Walters was impeded two or three times and not given the foul, they cleared their lines, we made a mistake by not defending the long ball correctly and they scored the equaliser.
"It was an obvious free-kick from my point of view and we asked the referee about it - he said he was trying to play an advantage, but it certainly wasn't an advantage to us.
"So the second half we are not happy with
The first half we were good value, but it is about managing the game."
While Stoke remained 18th, Leicester finished the game still in the lofty position of second as they preserved their unbeaten start to the season.
It was the fourth league match in a row they have salvaged something having gone behind - including a 3-2 win over Aston Villa last time out when they were also 2-0 down at the interval.
Foxes boss Claudio Ranieri had promised pre-match to buy his players pizza if they kept the first clean sheet of their impressive campaign.
And when asked about that after the match, Ranieri said: "No pizza, no hot dog, no nothing! They are maybe waiting for something more - wine, cheese..
It is unbelievable!
"I love a clean sheet - I am an Italian man!"
He added: "It was a great comeback, but it is not possible to do this every time.
"We started very well, but suddenly conceded and then made a mistake to concede the second.
"In the second half we reacted very well, but every time we must be very concentrated.
"It was important to show good spirit and character with the reaction - in the end that was good.
"But we said in the dressing room, if we score the first goal then everything will be possible."
Source : PA
Source: PA