I noticed in the code for WindCharge#explode():
https://hub.spigotmc.org/stash/projects/SPIGOT/repos/craftbukkit/browse/src/main/java/org/bukkit/craftbukkit/entity/CraftWindCharge.java#12

That the entity is not discarded.
Reviewing the NMS code, when MC uses explode() they also use the discard() method.

Suggestions:
(either would be good)
1) add the discard method within the CraftBukkit explode method
2) Make note in the javadoc that the entity is NOT discarded and you will have to manually do it yourself.

Sorry, I don't have test code to provide, I was testing this in a Skript based environment.