The issue was blamed on a technical problem with the software of an external service provider that instructs the officials as to which teams are eligible to play each other.
According to sources, Madrid were adamant that their pair should stand, even though the tie was drawn before the mistakes were made.
Madrid were drawn with Paris Saint-Germain in the round of 16.
A club source said that it was a lie that it was a software error. Human error begins with the second pair. The Real Madrid-Benfica was legal.
They contacted the European soccer body for a comment on Madrid's stance.
The situation was "surprising, regrettable and very hard to understand", according to the Director of Institutional Relations at Real Madrid.
We go into this tie with a lot of excitement. He told Real Madrid TV that the club and fans are aware of what this competition means. We're aware of the difficulties with the quality of players. The team will play well. They will be great for football.
The relationship between the two organizations was badly damaged this year due to Madrid's involvement in the proposed Super League.
The action against Madrid, Barcelona and Juventus was taken in April.
They were forced to suspend the proceedings after a Madrid court granted the Super League a preliminary injunction and referred the question of whether the clubs should be protected by free trade laws to the European Court of Justice.
Florentino Perez said during the club's annual general meeting last month that they might have to remind the European body of who Real Madrid are.
Real Madrid's history needs to be reminded of. Real Madrid has been involved in every necessary innovation over the years.
The current state of football leaves us no choice but to defend our interests.
