The Russian scored the opener in the last-32 first leg clash, with visitors Real going on to win 3-1 in a slightly surreal atmosphere as by that time news had travelled around the stadium about the threat of expulsion.
Cadiz subsequently reported Real to the Spanish football federation for breaking the rules, which would lead to expulsion from the cup.
However, Perez, having consulted the club’s legal team, now says they did nothing wrong.
“The ban for Cheryshev while a player for Villarreal is not effective as far as we are concerned as nobody had informed the player,” Perez told a news conference.
“Real Madrid did not know about it as we were not told by the player, Villarreal or the federation.
“This is a completely new situation for us because in the past when a player has had a sanction then they have always been notified. We have no reason to doubt him (Cheryshev) as it would be absurd if he had known about the ban and had played.”
A verdict is expected to be made by the federation on Friday.
It is the latest difficult incident so far this term for Real, who are stuttering in the league and lost 4-0 at home to arch-rivals Barcelona last month to lie six points behind the Catalan side after 13 games.
(Reporting by Tim Hanlon in Barcelona, editing by Mark Meadows)
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