I think there is already a report about this but I am unable to find it.
The EnderDragon destroys sometimes blocks that do not overlap with its hitbox. The blocks being destroyed are always right below the EnderDragon.
Replace the end stone in the End with for example dirt:
/fill ~-20 ~-15 ~-20 ~20 ~ ~20 dirt 0 replace end_stone
Dragon breaks blocks in far off locations!