If you use /summon to spawn an End Crystal to a coord containing a block other than air, it will spawn around that block. It's hard to describe; see the screenshot.
Steps to reproduce: Use /summon EnderCrystal x y z where (x,y,z) is presently a block other than air. (Notice that the one all the way to the right was summoned on a block of air, but the fire is missing.)
This may not be a glitch, since it's an entity and not a block, but IDK.
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No, that's just because the crystals bob up and down. I expected for the blocks they're in to be destroyed when the crystals were /summoned.
The point of putting multiple things in the screenshot was to show that it's not just by a particular block, it's by a wide variety. The last one is supposed to be air.
I don't understand the problem. The crystals in glowstone and the lamp are lower than the air one. Please clarify and write what you expected to happen.