I think there is already a report about this but I am unable to find it.

The bug

The EnderDragon destroys sometimes blocks that do not overlap with its hitbox. The blocks being destroyed are always right below the EnderDragon.

How to reproduce

Replace the end stone in the End with for example dirt:

/fill ~-20 ~-15 ~-20 ~20 ~ ~20 dirt 0 replace end_stone