The Potters had appeared to be on the way to a much-needed point at Turf Moor until Ashley Barnes netted a last-minute winner for the Clarets in the North-West.
However, Hughes has claimed that the Staffordshire-based team were unlucky to suffer a fourth setback in five matches, saying that an injury to Kurt Zouma influenced the end result.
The 54-year-old is quoted by Sky Sports News as saying: "Clearly it wasn't the result we wanted and it wasn't the result we deserved in all honesty. We restricted them to very few opportunities, I think their goal was the one clear shot we let them have the whole game. I thought our guys were magnificent in terms of standing up to the challenge.
"You know what you face here. It's not going to be clever football, it's not going to test you with clever movements and patterns, it's just challenging for long balls and you've got to be up for that. Unfortunately, we lost Kurt Zouma and I think that obviously that diminished our ability to compete for the balls in the air.
"In the end, they've got a little bit of fortunate, it seems to be shining on them at the moment, and that's all they need. The lad (Barnes) put a good strike on it and that's won the game for them but please don't tell me that anyone thinks they deserved to win that because they didn't."
Stoke sit in 15th position in the standings, just three points above the relegation zone.