The wind played a part in both goals, especially Asmir Begovic's opener after just 13 seconds, when the Stoke goalkeeper's long kick from his own box took one bounce and flew in over Artur Boruc's head.
Jay Rodriguez's downward header three minutes before the break then looped over Begovic for the equaliser as the two sides shared the spoils.
Hughes told Sky Sports News: "You don't expect to score under those circumstances and their goal as well, it was rather freakish - it seemed to hit (him) possibly in his face. It bounces up high and just creeps in, so (they were) two strange goals really.
"But it was a difficult day in terms of the conditions. The wind really played a part and of all the conditions that you can play under, wind is the one that will affect the game the most adversely and I think it did.
"In fact, it was probably harder to play with the wind than it was against it. I think that was borne out - Southampton played well in the first half, I thought we played well in the second half and that was against the wind. It was very difficult just to get the ball down and pass and move."
Hughes rued Ryan Shawcross' miss soon after the Stoke had taken the lead, with the unmarked defender volleying wide from close range after a corner with the goal gaping.
"Ryan Shawcross had a great opportunity right in the middle of the box. If we score that and it's 2-0, then it's very difficult for Southampton to come back," said Hughes.
"But they're a good side, I think everybody saw that today, they're well organised and have got good abilities so so all in all, we take a point out of the game under difficult circumstances."