The bug
If you blow up a (naturally-placed, at least) end crystal, its hitbox will seem to remain after it is destroyed and won't let you interact with the 2x2 area it was once on. Nothing shows up with /say @e[distance=..2] or when using F3+B, though (Image 5).
How to reproduce
Place an end crystal on bedrock (Image 1).
Punch it so it blows up (Image 2).
Examine the spot where the end crystal used to be. You cannot punch the bedrock (Image 3) or the closest half of the blocks next to it (Image 4).
Can confirm. Happens with both Bedrock and Obsidian as the base.
I tried running a /kill @e[type=!player,distance=..3] while near ghost area as well, no luck. It says no entities were found.
This ghost entity can be pushed via pistons, but not pulled using sticky pistons.
Looking at the area where the entity should be, the autocomplete for /data get entity will follow with a UUID, but the result will state that the entity cannot be found. I tried with /data get block but the game stated the target block was not a block entity.
TNT will not destroy the entity. There is no visible hitbot, and arrows will pass through.
The really strange bit is that I was able to duplicate it twice with no issue, went to the End, was not able to duplicate it, went to the Nether and it only worked in certain coordinates. Went back to the overworld and I was unable to produce it again. Entering / exiting dimensions also will unload the entity. Did not get to test yet if reloading the world will too.