Carlo Ancelotti claimed referee Mario Melero Lopez invented a decision to award Girona a penalty after Real Madrid were held to a 1-1 draw.
Los Blancos moved back above Barcelona to the top of the table but dropped points for only the second time in LaLiga this season.
Vinicius Junior put the champions in front in the 70th minute at the Santiago Bernabeu on Sunday, but Cristhian Stuani equalised from the spot 10 minutes later.
Referee Melero Lopez adjudged Marco Asensio handled in the box after a VAR check and there was more late drama, with Rodrygo having a goal disallowed as Paulo Gazzaniga was deemed to have had control of the ball with one hand when the forward poked it into the back of the net.
Toni Kroos was then sent off for the first time in his club career in stoppage time as Madrid slipped up, but Ancelotti felt they were hard done by.
The Madrid head coach said: "I never like to talk about the referees, but today I am going to. I have spoken with Asensio and it is very clear that he does not touch the ball with his hand, it hits him in the chest.
"It is true that the position of his left hand is a little strange, but it covered the body, it did not make it bigger. There may be doubt if he touches it, but he simply did not touch the ball with his hand. This penalty is an invention."
Ancelotti conceded Madrid fell short of the standards he expects after they slipped up on the back of a Champions League defeat at RB Leipzig.
The Italian expects a response when they face Celtic on Wednesday, when the holders can secure top spot in Group F.
He said: "We're not at the level we were last week, we've had some problems, with the return of injured players, Rodrygo, [Luka] Modric, [Aurelien] Tchouameni.
"We're playing a lot of games and we're feeling tired. they have affected us a lot. We have the opportunity on Wednesday to be first and the goal is to be leaders at the break. At the moment we have everything in hand."