In our specific world (mega link below), throwing objects (eggs, arrows, dropped objects, etc) through the nether portal from the surface crashes the server. Our portal on the surface is near the world spawn. You can consistently crash the server if you spam eggs at it.

We haven't properly tested it, but I'm told that if somebody is in the nether on the other side of the portal, the server doesn't crash when a surface person throws eggs through. The portal on the surface (but not in the nether) is a square shape, if that matters.

We messed around with the portals and now it doesn't crash. We're not sure specifically what fixed it. The zip below contains all the server files. I stopped the server and zipped it immediately. Same deal as the "crashy" server, all files included in zip.

Crashy:
https://mega.co.nz/#!q89x2bIS!9XmRxyfsHUPAZktw3hQ5i5rGb1o3OXkEM5ojFz7atWQ

"Fixed":
https://mega.co.nz/#!v9sVHYDR!wiAFJgsMI7DgPJuy9YuU62LgShb5DMogZrznB2mXtqg