#5 Injuries and lack of Squad Depth
Injuries have been the main reason behind the downfall of this team. Right when the team had started playing as a cohesive unit, crucial players were hit with injury. Bale as always was one of the first to be injured followed by Isco and so on, and this led to Lopetegui's downfall.
With such crucial attacking players injured it shouldn't have as a surprise when the goals dried up. This wouldn't necessarily be a problem had proper backups been available as was the case in the LaLiga title-winning season under Zidane.
Players such as Rodriguez and Morata are game changers and they helped the team get over many a crunch situation. Injuries are part and parcel of the modern day and no team can hope to win a title without proper backups and Real Madrid at this moment precisely lacks backups.
The task and challenge at hand for the next manager of Real Madrid is a big one.