The hosts were furious when their penalty appeal was turned down after Glenn Murray fell under a Ryan Shawcross challenge but they levelled in the 44th minute as Pascal Gross slotted the ball home after a fine solo run and cross from Davy Propper.
"When you have been behind twice you have to show character and we did", Hughton told Sky Sports.
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The Argentinian added: "The objective was to qualify and we've achieved that, and now it's important to finish first if we can". I will tell Dele now". "I think the referee has moved on but always this is always good to know".
And for Stoke manager Mark Hughes, it also meant his side avoided equalling the club's worst Premier League start after 12 games.
"Credit to the players, you had a Stoke team who at times were very happy to defend their own half". Our levels weren't perhaps what they've been in other games.
The visitors took the lead in the 27th minute through Cameroonian global Eric Choupo-Moting who capitalised on poor defending to put Stoke ahead after he was set up by Xherdan Shaqiri.
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"I don't think you can afford to target taking points from specific matches. It probably was a penalty", said Shawcross.
Colombia winger Jose Izquierdo earned the promoted team a point with a 60th-minute goal, scoring at the second attempt after his initial cutback was cleared.
A loss of concentration in first half added time, however, ensured Stoke restored their lead before the interval after a Fletcher corner again caused problems with the ball bouncing towards Zouma who headed home from close range. So too did Mark Hughes, his opposite number, who saw his side fail to hold on to the...
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"Any away point gained is a good result usually, but having got into a winning position twice that's where the disappointment lies". We endeavour to entertain and try to win as many games at home as we can.