He is still furious that Andy Carroll is having to serve a three-match ban after receiving a red card in the 2-0 Premier League home win over Swansea on 1 February.
An independent tribunal upheld the FA's decision to reject the Hammers' appeal against Carroll's sanction after he had tangled with Chico Flores.
Carroll sat out the win at Aston Villa on Saturday and Allardyce will again be without the totemic striker for the midweek game against Norwich City.
Allardyce told Sky Sports News: "I'm upset about the injustice after, as well as the original decision. I think we've been dealt a total injustice in the game of football.
"We've done all we possibly could to avert that injustice but we have to accept it unfortunately. My only hope is that the referees' system becomes better because that is obviously flawed in this situation.
"I think that the disciplinary hearing can be looked at and become better after that injustice. Of course after we went to the FA and the tribunal scenario, I don't know the outcome of that because I wasn't involved.
"Hopefully if I am, maybe they will help to get a better system in place because things like that decision should not happen in the professional game as they happen for me."
West Ham have climbed to 15th in the league on the back of a seven-point haul from the last three games and Allardyce is happy to be able to bolster his squad for Norwich on Tuesday.
"First and foremost, we have to maintain our defensive stability and if we do that, we'll have a great chance of gaining another three points," he added.
"I'm pleased to report that Mo Diame and Joe Cole are back in the squad for this one too. We're in a rich vein of form at the minute which has been helped by players coming back into the squad.
"Every game recently has been massive in terms of trying to get the team in a better position in the league."