These things don't happen often, but the fact that they do and almost always play into Real's hands is a fact. But nothing can be done about it, until they are found to be doing it deliberately everyone will just forget about it a week after the match. In such cases there is only one way out - to beat Real Madrid in this match, that no decisions of the referee could not affect the outcome of the match.
It seems to be a fact indeed. Maybe it is worth to do a little search whether someone ever took the time to analyze wrong referee decisions which led to a decisive advantage among the big teams in Europe. But I agree without knowing any data, it often looks like Real Madrid seems to have some leverage over referees. Besides just perceiving it like that, there has been evidence a while ago I think that referees have been paid millions and then those payments were declared as "advisory services". That's of course unbelievable.
But considering how big of a club is, imagine you are a referee in a game in the Bernabeu Stadium and you blow the whistle to the disadvantage of Real Madrid. This could mean you never can show up in the stadium again, depending on how important the game is. The pressure is real for those referees.