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.