I am using a custom inventory gui. The NPE is thrown if I cancel an InventoryClickEvent because I do not like the player to click an item.

InventoryWrapper.splitStack sets an item to null. This always leads to given NPE. I found the Problem in my 1.11 and 1.12 Installation. Maybe it is present in older releases.

Caused by: java.lang.NullPointerException
 at org.bukkit.craftbukkit.v1_11_R1.inventory.CraftItemStack.asBukkitCopy(CraftItemStack.java:60) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at org.bukkit.craftbukkit.v1_11_R1.inventory.InventoryWrapper.setItem(InventoryWrapper.java:76) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at org.bukkit.craftbukkit.v1_11_R1.inventory.InventoryWrapper.splitStack(InventoryWrapper.java:46) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.Slot.a(SourceFile:101) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.Container.a(Container.java:287) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.PlayerConnection.a(PlayerConnection.java:1847) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.PacketPlayInWindowClick.a(SourceFile:33) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.PacketPlayInWindowClick.a(SourceFile:10) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at net.minecraft.server.v1_11_R1.PlayerConnectionUtils$1.run(SourceFile:13) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) ~[?:1.8.0_111]
 at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[?:1.8.0_111]
 at net.minecraft.server.v1_11_R1.SystemUtils.a(SourceFile:46) ~[spigot-1.11.2.jar:git-Spigot-7d78b81-e2a288c]
 ... 5 more