When certain block entities are placed then the player leaves the chunk and unloads them, upon returning, several block entities may be glitched. Exiting that world and reentering it will fix all problems.

Chest/Locked Chest/Ender Chest: When opening, there appears a second chest that is closed within the same block. Breaking chests after unloading and reloading will cause a "ghost" chest to remain.

Spawners: Each unloading and reloading causes another of the spawner's mob to appear inside the spawner. Breaking spawners after unloading and reloading will cause a "ghost" mob from the spawner to remain.

Enchantment Tables: Each unloading and reloading causes another of the book entities to appear on the table. Breaking enchantment tables after unloading and reloading will cause a "ghost" book entity to remain.

Beacons: A 'ghost' beam remains that is visible when changing the beacon color, as you can see the old one glitching with the color of the new one. Breaking beacons after unloading and reloading will cause a "ghost" beacon beam to remain.

Signs: Breaking signs after unloading and reloading will cause a "ghost" sign to remain.

Heads: Breaking heads after unloading and reloading will cause a "ghost" head to remain.

Other block entities may or may not have something occurring to them but may not be visible.