When shot with an arrow, the Ender Crystal will explode as expected, but the two floating cubes and the entity base will remain and the surrounding area will flicker rapidly; having multiple destroyed crystals in the same area can cause severe lag. The bedrock block caused by the crystal being destroyed also will not spawn.
Attached screenshot shows the "destroyed" Ender Crystals.
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An ender crystal is the slab-like piece of bedrock and the two floating cubes. It normally spawns on top of bedrock. What I think happened is you somehow destroyed the bedrock instead of the crystal.
I have played this map and can confirm it, however, in The End, in Creative and Survival they work as expected too, exploding and nothing else. This may be an issue with the map, you could talk to Vechs about this.