Danny Ings scored twice in as many minutes for the visitors at the Britannia Stadium as Sean Dyche's side stunned their Premier League opponents in the early stages.
From that point, Stoke dominated the game and pulled a goal back through Jonathan Walters' header shortly after the half-hour mark.
Despite enjoying the vast majority of possession and delivering numerous dangerous deliveries into the box, Stoke were unable to force an equaliser as Burnley recorded back-to-back Premier League wins.
And Hughes was in no doubt as to the reason why his side fell to defeat.
"Unfortunately we lost this game because of the first 10 to 15 minutes where we didn't really get to grips with what the opposition were likely to do," he said.
"We talked at length before the game, telling the guys what to expect and in that period you've got to be rock solid and that gives you the platform to kick on.
"But unfortunately we can put it forward as an excuse. We had a makeshift back four in terms of being able to work with them prior to the game.
"We had to move things around this morning when Erik Pieters failed a fitness test but even so we had enough quality and experience at the back to deal with the situations that we allowed Burnley to create.
"In that first period we gave them two great opportunities through collective and individual errors and they took them.
"If you allow that in the Premier League you're likely to concede and that's happened on a number of occasions this year which is the frustrating thing for us because what happens then is your game changes, your mentality changes.
"It becomes a little frenetic and that patience isn't there and as a consequence it's more difficult to manage the game.
"The top and bottom of it is we gave ourselves too much to do."
