Brian McDermott claims an official said his Reading side should have appealed more when Demba Ba equalised against them for Newcastle with what seemed a clear handball.
McDermott's side were leading 2-1 at home with seven minutes to go on Saturday, but the striker's goal denied them their first Premier League win of the season.
And the Royals manager said the fourth official had suggested that a stronger appeal from his players could have seen the goal chalked off.
"I feel a sense of injustice because there was an injustice - obviously the goal shouldn't have stood,'' he said.
"My concern slightly, or more than slightly, is the conversations with two people now... the match delegate at the Chelsea game (which Reading lost 4-2) said that my players didn't appeal for the [Fernando] Torres offside goal, and the fourth official said to my goalkeeping coach that only two of my players appealed [against Newcastle].
"For me, it is very difficult to take that. What are we asking? If we appeal for every decision we might get one or two?"
McDermott said the "last thing" he wanted was for "our players to start trying to referee the game". He said Reading "have to let the referee and the assistant referees get on with their jobs, and that is what we are trying to do".
Reading travel to Swansea as they continue their search for a first league win. The Swans denied them a place in the top flight with a 4-2 win in a thrilling 2011 Championship play-off final, but McDermott said revenge was not on his mind.
He explained: "I'm not into revenge. It is a game of football which, on the day, we lost. Swansea won the game, and history is history.
"The time wasn't right for us then - it was right for us last season - so there is not even a thought of that in my mind. All we are trying to do is go there and put in the right performance."