The Spaniard is under huge pressure after just two points from his first nine league games as Owls manager, with chants for him and owner Dejphon Chansiri to leave during a humiliating televised 3-0 defeat to Sunderland.
The Owls have not helped themselves by conceding four penalties in that time – Bambo Diaby brought Mason Burstow down for Jack Clarke to score a penalty in Friday's game.
The previous week a penalty converted by Jamaal Lowe after Pol Valentin's 28th-minute foul on Josh Ginnelly opened the door to another 3-0 defeat, at Swansea.
Surprisingly, Munoz says the Professional Game Match Officials Limited have apologised for that.
"One of the good thing last week was that the referees called us to say they were so sorry because it was not a penalty against Swansea," said Munoz.
"They said they were sorry about the situation."
Ginnelly certainly made the most of contact from Valentin as he ran into the penalty area from the side, but side-on pictures showed a clear pull of the shirt by the wing-back, so it is surprising the PGMOL took the Owls' side over Anthony Backhouse, who is on fourth official duty for Preston North End versus West Bromwich Albion this weekend.
But Munoz conceded his players have to stop getting themselves into situations where they are vulnerable to mistakes by themselves or the officials leading to spot kicks.
"I don't speak about the referees but sometimes we need to stop these situations – sometimes it's stress, sometimes it's stupid things – like against Cardiff when the ball was where it was," he said, referring to August's 2-1 defeat decided by a stoppage-time spot kick.
"You can never understand exactly why they happen but you try to find a solution to stop the situation happening.
"We need to be more comfortable on the pitch, we need to feel like it's a normal game. We have 37 more and the pressure on everyone on Friday was like it was a final."