BUG #1
Step 1 - creating and opening custom inventory [tested on brewing, hopper, workbench, dispenser, enchanting] (works fine):
Inventory inv = Bukkit.createInventory( player, InventoryType.BREWING, "test" );
player.openInventory( inv );

Step 2 - shift clicking on item (error) [tested on brewing, hopper, workbench, dispenser, enchanting]
??[14:40:32] [Server thread/FATAL]: Error executing task
java.util.concurrent.ExecutionException: java.lang.StackOverflowError
at java.util.concurrent.FutureTask.report(Unknown Source) ~[?:1.8.0_25]
at java.util.concurrent.FutureTask.get(Unknown Source) ~[?:1.8.0_25]
at net.minecraft.server.v1_8_R3.SystemUtils.a(SourceFile:45) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.B(MinecraftServer.java:714) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.DedicatedServer.B(DedicatedServer.java:374) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.A(MinecraftServer.java:653) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.run(MinecraftServer.java:556) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]
Caused by: java.lang.StackOverflowError
at net.minecraft.server.v1_8_R3.RegistryMaterials.b(SourceFile:48) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.Item.getId(SourceFile:52) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at org.bukkit.craftbukkit.v1_8_R3.util.CraftMagicNumbers.getId(CraftMagicNumbers.java:70) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.ItemStack.setData(ItemStack.java:324) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.ItemStack.<init>(ItemStack.java:64) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.ItemStack.cloneItemStack(ItemStack.java:445) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.Container.clickItem(Container.java:257) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.Container.a(Container.java:447) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.Container.clickItem(Container.java:259) ~[spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]??

BUG #2
Step 1 - creating custom anvil inventory, and opening it for player(works fine)
Inventory inv = Bukkit.createInventory( player, InventoryType.ANVIL, "test" );
player.openInventory( inv );

Step 2 - clicking on any slot with mouse1(error)
??[14:50:05] [Server thread/FATAL]: Error executing task
java.util.concurrent.ExecutionException: java.lang.IndexOutOfBoundsException: Index: 24, Size: 0
at java.util.concurrent.FutureTask.report(Unknown Source) ~[?:1.8.0_25]
at java.util.concurrent.FutureTask.get(Unknown Source) ~[?:1.8.0_25]
at net.minecraft.server.v1_8_R3.SystemUtils.a(SourceFile:45) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.B(MinecraftServer.java:714) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.DedicatedServer.B(DedicatedServer.java:374) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.A(MinecraftServer.java:653) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at net.minecraft.server.v1_8_R3.MinecraftServer.run(MinecraftServer.java:556) [spigot-1.8.8.jar:git-Spigot-d97e08b-880a532]
at java.lang.Thread.run(Unknown Source) [?:1.8.0_25]??