Barcelona cruised by Real thanks to a superb second-half performance that saw three goals come for the La Liga leaders.
A Dani Carvajal red card and the subsequent penalty made the result safe for Barcelona as Real were beaten in front of their home fans in Madrid.
Isco did not get the chance to play in the game, despite Zinedine Zidane using all three of his substitutes.
Gareth Bale, Marco Asensio and Nacho were called upon from the bench and Spanish publication AS claimed that Isco refused to continue warming up when Real were chasing the game.
AS claimed the sight of Nacho coming on for Karim Benzema prompted Isco to return to the bench and suggested Zidane will have been furious to see his playmaker decline to be subbed on.
But, Isco has now hit back at that report and insisted Zidane had already informed him what the final two substitutions would be.
He said: ‘Stop spreading sh** I knew my other two team-mates were already going to be subbed on.
‘I didn’t know four substitutions were possible.’
Reports in Spain have hinted at discontent in the Real dressing room between Isco, Cristiano Ronaldo and Zidane.
More: Real Madrid
Isco starred for Real in the absence of the injured Bale, but he and his team-mates have struggled for form in La Liga.
The loss to Barcelona leaves Real 14 points behind their bitter rivals and it seems Los Blancos could be out of the title race just a few days before the turn of the new year.
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