Keith Hill criticised referee Stuart Attwell after Barnsley were beaten 1-0 by Sheffield Wednesday in the Yorkshire derby at Oakwell.
Chris O'Grady netted the only goal in the 35th minute to leave the hosts without a win in 11 games and still inside the relegation zone.
However, Barnsley felt the goal should not have been awarded as Gary Madine appeared to foul keeper Luke Steele during the build-up.
Manager Hill said: "The referee gets it wrong and the ramifications of him getting that decision wrong could be catastrophic. The result has been decided by that decision.
"In the second half we had more than enough opportunities to get something out of the game.
"I just thought it was a difficult game for the referee. He will be disappointed with his performance when he comes to digest it.
"Unfortunately, I don't have a second job to go to on Monday and I have to deal with it.
"It's happening on too many occasions that games are being decided by catastrophic refereeing decisions and we have been on the end of too many.
"I was pleased with how the players handled the occasion and I saw us strive to get something out of the game but unfortunately it didn't materialise."