Real won 3-1 at third-tier Cadiz on Wednesday but fielded the suspended Denis Cheryshev.
The winger faced a ban carried over from last season when on loan at Villarreal and elimination is the punishment for breaking Spanish federation rules.
"We found out at halftime and took him off then as we wanted to do the right thing," Real coach Rafa Benitez told a news conference.
"The club didn't know anything beforehand. We weren't told by the federation or Villarreal."
It comes only a few months since Real were also left red faced by the collapse of the David De Gea and Keylor Navas swap deal with Manchester United, as time ran out at the end of the transfer window.
It was always going to be a tough task for Benitez to win over the players and fans following the dismissal of the popular Carlo Ancelotti and the team has stuttered this season to provide the scintillating attacking football demanded by the Bernabeu faithful.
The pressure on Benitez was increased by a humiliating 4-0 home defeat by Barcelona last month and now Real are down in third place in La Liga, six points behind the Catalan leaders.
Benitez also has to contend with a heavily depleted defence against Getafe with Sergio Ramos, Raphael Varane and Marcelo in the treatment room.
Barcelona are going from strength to strength and take on a Valencia side in disarray on Saturday following the resignation of coach Nuno Espirito Santo.
Former-Manchester United and England defender Gary Neville was the surprise choice to replace him but he will not take over the reins until Sunday and it will be interim coach Salvador Gonzalez in charge, assisted by Phil Neville.
Deadly trident Lionel Messi, Neymar and Luis Suarez will be primed to build on the 125 goals they already have this calendar year having been rested in Barca’s 6-1 rout of third tier Villanovense on Wednesday to book a place in the last 16 of the cup.
(Reporting by Tim Hanlon in Barcelona, editing by Justin Palmer)
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