Peter Odemwingie has caused his manager several headaches since his extravagant attempts to force through a move to QPR in January and was greeted angrily by fans after being sent to warm up.
Clarke could not confirm whether Odemwingie exchanged words with the crowd, but admitted the incident prevented him sending the forward on.
"There was a bad reaction, the crowd let their feelings be known," he said.
"I don't know (the details) because I was watching the game. I asked him, Jerome Thomas and James Morrison to get prepared and I wanted to put on two from three.
"When he went out the warm-up there was a negative reaction and if I'm honest the crowd reaction made me go with James and Jerome.
"I still think Peter's got a part to play in some matches but we'll deal with it from game to game."
Callum McManaman was Wigan's match-winner, sealing the points 10 minutes from time after superb play by the electric Shaun Maloney.
Prior to that, Arouna Kone and James McArthur twice drew Wigan level following goals from Shane Long and Gareth McAuley.
- Sports & Recreation
- Peter Odemwingie
- Jerome Thomas