This page lists plug-ins that do not work very well alongside this plug-in or do not interact well. This list is far from complete because I can't test my plug-in with every single other plug-in.
The ItemFixer plug-in removes all kinds of 'cheated' properties of items like nbt tags and impossible enchantments. Since all custom items have such 'cheated' properties, this will cause all custom items to remove their texture and special properties as soon as any non-op player holds it in their hand.
The ExploitFixer plug-in prevents all kinds of exploits, including hacked creative items. Unfortunately, it considers all custom items to be hacked creative items, and removes all their special powers and their texture.
Luckily, this only happens in creative mode, so this won't be a problem if players don't need to be in creative mode. To prevent this anyway, you can disable itemsfix in the config. The drawback of this is that players in creative mode can obtain any item they want. (But note that players can give themselves stacks of diamond blocks anyway, so you should be careful with giving players creative mode even if you keep itemsfix enabled).
The UltimateStacker plug-in will quickly fill up your inventory when you pick up a stack of custom items. You can work around this problem by disabling item stacking in its config.
To prevent custom items from being used in vanilla crafting recipes, this plug-in will block any attempt to use custom items as crafting ingredients that is not registered as custom crafting recipe in the editor. Unfortunately, this also prevents other crafting recipe plug-ins from using custom items in their recipes. All crafting recipes with normal ingredients should still work though.
Using other custom item plug-ins alongside this plug-in is probably going to cause trouble, especially if they also have custom textures. If that other plug-in uses the same mechanism for custom textures as this one, weird effects can occur.
When using a custom item from this plug-in as crate key, it may or may not happen that it will lose its texture and its custom item properties upon restarting the server. I don't know why or under which circumstances this happens, but this is how you can prevent it from happening: Add PublicBukkitValues.excellentcrates:crate_key.id = THE_KEY_NAME to the extra NBT of the custom item, for instance:
(In this example, the name of the key is oy_kasasi_anahtari)