I created a superflat world with and end style and after a long time flying around I found this wrongly generated ender crystal (screenshot-1.jpg, foreground).
The wide part of the bedrock block (belongs to the crystal) should be at the bottom (like at the crystal at the back, same image)

Technically the crystals are only 1 block higher than they should be.

creation template for that superflat world:
2;7,60x121;9;village,decoration,dungeon,lake,mineshaft,lava_lake

EDIT: After reloading the world (to check the creation template) the crystal corrected it's position tho someone should look after that.