With 13 minutes remaining at St Mary's Stadium and the scores level at 1-1, the midfielder was shown a second yellow card for diving in the penalty area.
The hosts looked to have held on for a point, but Harry Maguire went on to score the winner in stoppage time and inflict a second successive defeat on Saints.
"In my opinion, going down to 10 men was unfortunate," Hughes told BBC Sport at full time.
"To defend Pierre, I think both yellows were a bit soft. The first one was just a coming together. But if you've got one, you walk a tightrope.
"I think he was clipped when he went down on the second, but Mr Moss was in position and he sent him off."
Southampton travel to south coast rivals Brighton & Hove Albion in the second round of the EFL Cup on Tuesday before visiting Crystal Palace in the Premier League next Saturday.