#1 Zidane's tactical shortcomings
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Zinedine Zidane has won 8 trophies in 2 years at Real Madrid. However, it is a well-known fact that Zidane is more of a man-manager instead of a tactical genius.
In last 2 years at Madrid, Zidane has failed to put a proper system at a place in Madrid. He is a pragmatic coach who makes the team play as per opposition. That is possibly one of the reasons why Madrid in last 2 years have found it hard against weaker teams and it was an individual quality that took them through on most occasions. But this season, that hasn't happened and hence they have suffered.
Zidane's failure to put a proper system has affected Real Madrid. Thus even after having some of the best individual talents, they have struggled as a team. Whether it is about attack or defence or midfield there are evident shortcomings which Zidane has failed to repair. This season, even after repeated failures he has failed to bring in changes to make the team perform again.
Zidane's inexperience and failure to bring in changes have had an adverse effect and it remains to be seen whether he can bring in changes required to get Real Madrid back on track and if he is not able to do that, it remains to be seen whether Madrid's board and Perez are patient enough or not.