Tom Clarke was adjudged to have handled Franck Moussa's cross and Lee Barnard converted the resultant spot-kick to give the Shrimpers their 11th win in 14 league matches.
Clark said: "I don't understand where the players are meant to put their arms in the penalty area. I felt for Tom Clarke because I thought he played well and he didn't deserve that.
"To be fair to the referee I thought he handled the game in general terms very well but big decisions change games.
"It's a bit disappointing to lose in that manner. We didn't deserve to win the game. It was a 0-0 game. We didn't work their goalkeeper enough and our attacking players didn't produce performances like they have done in the past."