The Rovers manager highlighted a penalty for handball awarded by referee Peter Walton earlier this month against Tottenham as an example - though in that game Blackburn came back from a goal down to win.
Allardyce said: "We have had to overcome some very bad decisions by the officials - some have cost us points and some haven't.
"Against Tottenham there was a penalty given by the referee who made a massive wrong decision on the day. He has since said that he still thinks he made the right decision and that is a bizarre scenario.
"He got it horribly wrong and that's what I hope doesn't happen when we play Wigan.
"We don't want that sort of uncontrollable situation going against us against Wigan and we hope the referee Steve Bennett is consistent in his decisions and that if there is a major decision it doesn't go against you and is given the right way."
Rovers will again be short of strikers on Sunday with Roque Santa Cruz and Jason Roberts both still on the injury list.
There are now doubts over whether Santa Cruz (knee) and Roberts (metatarsal) will play again for Blackburn this season - or in Santa Cruz's case ever again given that he looks certain to be sold in the summer.
Allardyce has no fresh injury concerns but accepts both strikers could miss the rest of the season.
He said: "There is a chance we might not get Roque back and there is a chance we might not have Jason either. So we have to accept as we go along those players are not available.
"It's going to be a difficult decision as the weeks tick on. We don't want to have to rely on risking a player who may not be 100% fit."
Blackburn should also have a bigger crowd than usual for a Sunday game after offering entrance to the last three home matches of the season for just £20. Of the 4,000 seats available, 3,200 have been sold.
Blackburn 10/11, Draw 12/5, Wigan 16/5