The 59-year-old remains angered by the decision to uphold a three-match ban against Andy Carroll, who was controversially sent off against Swansea City last week when referee Howard Webb deemed he had struck Chico Flores with his arm.
An independent tribunal subsequently backed the original decision of the FA's disciplinary panel on Friday, meaning Carroll missed the 2-0 win at Aston Villa, and will sit out the matches against Norwich City on Tuesday and Southampton at the weekend.
West Ham captain Kevin Nolan believes Carroll was the victim of an "injustice" - a sentiment echoed by his boss Allardyce, who has called for a review of the current system.
"I'm upset about the injustice after, as well as the original decision," he said. "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."
Elsewhere at West Ham, an agreement has been reached over the sale of Upton Park to local developers ahead of the club's proposed move to the Olympic Stadium in 2016.
The Galliard Group were chosen from the bidding process, with vice-chairman Karren Brady saying their willingness to uphold the traditions of the club was key to the agreement.
She told the club's official website: "We opted to reach an agreement with Galliard because they are a local London developer and employer with origins in east London.
"The deal demonstrates that we have been true to our word by securing the regeneration of two areas of east London through our move to the Olympic Stadium in 2016.
"In addition, and most importantly for us, we can see that Galliard are passionate about working with West Ham United to engage their supporters to help deliver a fitting legacy that will honour the tradition of the famous ground.
"We are confident that West Ham United fans will be excited about their vision and the way they plan to respect more than 100 years of West Ham history at Upton Park."
