The Potters had secured a two-goal advantage but allowed Swansea to take the lead before a controversial handball award allowed Charlie Adam to score a penalty to rescue a draw
Stoke surged into a two-goal first-half lead at the Liberty Stadium courtesy of strikes from Jonathan Walters, on his 100th consecutive Premier League start, and Stephen Ireland.
Yet Swansea hit back to lead 3-2 with the aid of Wilfried Bony's brace before a disputed injury-time penalty from Charlie Adam ensured the spoils were shared.
While Hughes saw promise in his team's performance in the opening period, he does not want to see a repeat of the defensive failings that enabled Swansea to hit the front.
"First half, I thought we were excellent - we came with a game plan and really executed it well," Hughes said.
"But second half, obviously we knew that there would be a response from Swansea and certainly there was - credit to them.
"They put us under pressure and, from my point of view, we're disappointed we didn’t deal with that pressure as well as we could have.
"Obviously to concede three goals in the manner we did wasn’t what we've been about this season to be perfectly honest with you; we have only conceded, prior to today’s game, 11 goals in the Premier League in 10 games so defensively we have been fine.
"In that second half, I just felt we lost a little bit of energy. We had to substitute Stevie Ireland and Wilson Palacios because of injury, [and] Marko Arnautovic we just couldn't get in the game so we made a change there and I felt that unfortunately hindered us.
"The substitutions that Swansea made gave them a little bit more energy. The momentum of the game totally shifted in the second half and we didn’t deal with it so that’s a lesson for us to learn that we can't allow that to happen in the future."