I was playing on a server and i threw an enderpeal at a nether portal (in the overworld) (in spawn chunks if it matters, i didnt check).
The result was the server crashing and then the chunk of the portal block it hit resetting and the portal block in the nether resetting the chunk
1. throw enderpearl at a portal ON A SERVER
2 see results, halving the portal (as you can see in the screenshot)
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im sure that its totally vanilla (it might be 1.8.3, im not sure), though under the chunk that reseted there were command blocks on 1 tick cycles... IDK but you agree its weird
Are you sure that the server is a vanilla one? I just tested this on my local (vanilla) server and nothing happened,
I did exactly what you did on a spigot server before and it crashed too, maybe thats the case?