Denis Cheryshev, who scored the opening goal in the 3-1 win, should have been suspended after he received three yellow cards in the competition for Villarreal last season.
Cheryshev was withdrawn from the action moments after half-time, when Real had realised their error, with head coach Rafael Benitez saying they wanted to “show good faith”.
The former Liverpool and Chelsea boss added: “The club had no idea. The federation did not let us know and as soon as we found out we substituted him.”
Last season Osasuna were kicked out of the tournament for playing an ineligible player while Benitez was in charge of Valencia when they were disqualified from the Copa del Rey having played too many non-EU players in a tie in 2001.
But Perez believes that as neither the player nor the club were informed of the suspension that Real cannot therefore be disqualified from the Copa del Rey.
Perez said: “The one-match ban for three yellow cards in our view is not effective because no-one has notified the player as specified in item 41.2 of the Disciplinary Code of the RFEF.”
Earlier, Cheryshev confirmed he did not receive notification from his former club that he would be banned.
He said: “I did not receive any notification from Villarreal to inform me that I had been banned from playing in the Copa del Rey.”