Winger Jose Izquierdo levelled for the second time, cancelling out Kurt Zouma's header following Eric Maxim Choupo-Moting's opener and Pascal Gross's equaliser.
Before the win at Swansea, the Seagulls recorded a 3-0 hammering of West Ham, prompting Hughton to say "We're on the back of two away wins, which is something that gives us a lot of gratification and to now get back-to-back wins would show the level we're playing at and our capabilities as a squad". They're a very manly team and I didn't think we probed enough.
And Stoke capitalised on that let-off just before the half-hour mark - Choupo-Moting providing a cool finish after Lewis Dunk failed to deal with Xherdan Shaqiri's hopeful lofted ball.
The hosts seemed to have ensured that they would go into the break level when Pascal Gross equalised, but Stoke responded nearly instantly through Kurt Zouma - the on-loan Chelsea defender getting his first goal for the club. The referee didn't have the best angle.
The impressive Davy Propper tiptoed past four Stoke defenders before being forced out wide, from where he laid the ball back for Gross to smash through the legs of Lee Grant. "Brighton didn't create too much of note so we are disappointed with the goals we conceded", said Stoke boss Mark Hughes.
But moments later Stoke retook the lead, Choupo-Moting heading Darren Fletcher's corner back across goal for Zouma to nod home his first Potters goal.
"Any away point gained is a good result usually, but having got into a winning position twice that's where the disappointment lies".
"We would have liked more".
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