Video: https://www.youtube.com/watch?v=C26u_u9OGSk

The Ender Dragon's block destroying ability is affecting locations that the Ender Dragon has never flown near.

What should happen: With the player standing near the exit end portal (0, 64, 0) in the End dimension the Ender Dragon will roughly travel in an area from the tops of the obsidian pillars to the location of the player. If the air is replaced with glass we can see where the dragon destroys blocks. The area in which the Dragon destroys blocks appears as a smoothly winding tunnel that follows the dragon's flight path.

What actually happens: The Ender Dragon's travels about the area as described above but the area in which the blocks are destroyed do not represent the flight path in which the dragon flew! When the dragon flies just beyond the obsidian pillars he will turn around a start heading back towards the middle. As the dragon makes that outer turn the tunnel shape path, which is caused from the dragon breaking the blocks, that is following the dragon makes an unexpected vertical tunnel (see images).

These tunnels can go from Y0 to Y256. They are unnaturally vertical with gentle curves. They are similar diameter to the tunnels caused by the dragon's natural block destroying ability. These vertical tunnels occur when the dragon makes sudden turns and are most noticeable at 0,0 and at the four intermediate directions (N/E,N/W,S/E,S/W).

These vertical tunnels of block destroying are not to be mistaken with the sloping looping tunnels caused by the dragon ascending or the dive bomb tunnels from the dragon descending.

Replicate by:
1) New survival world
2) goto The End
3) under the main End island fill in the area from 50,0,50 to -50,0,-50 with stone
4) set the player near the exit end portal (0,64,0)
5) AFK there a while as the Ender Dragon does its normal flight paths
6) check the stone area under the main End island for unexpected vertical holes in it.

Code analysis by marcono1234 can be found in this comment.