Reid said in the Yorkshire Evening Post: "That one decision changed the game. The goal should have been disallowed.
"I just don't accept that it was right to give the goal. We work for hours on the training ground perfecting that so we leave players in an offside position at a situation like that.
"The players have done exactly as we asked, but still been punished. I'd have been surprised if it had been given the other way."
Liverpool boss Gerard Houllier sympathised with the decision and agreed that it had changed the game. He said: "I can understand Peter's view on that second goal. I would have been disappointed myself. It was a turning point and it certainly helped us."
On tomorrow's cup-tie with Man Utd Reid said: "We've only a couple of days, but the players have got to pick themselves up because we've got another big game.
"These players have now lost to Liverpool and Manchester United and they were very disappointed in the dressing room on Saturday, but we can't dwell on it. We have to get on.
"We are not getting the rub of the green. Things haven't been going for us at all, but we've just got to get on with things.
"They say luck evens itself out over a season and I just hope that's the case because we haven't had much so far."