I have a world that was originally created with 1.9.2 Vanilla and moved to 1.9.2 Spigot. I have since moved it over to 1.11 Spigot. I am noticing that some times the end cities to do generate properly (more than half the city is missing), and/or the loot in the chests, elytra, potions in the stands, are missing. Mojang states that they are not able to re-create my findings. Here is the information that I provided to them.

Seed: -8913466909937400889
Location of End City: -1497, 147, -2725

This is the location of the ship where there was nothing in the brewing stand, nothing in the chests, and no Elytra