This bug only exists if the plugin is using in "compatibility mode" ("api-version: 1.13" was not added to the plugin.yml). If it is not running in "compatibility mode" everything is working correctly.

If I am putting an item into the inventory and the user clicks on it and my plugin is listening to the InventoryClickEvent and I am using equal to check if the item, which the player clicked on, is equal with the item, which I did put into the inventory, it tells me that they are not equal even though they obviously are equal.

To prove that the bug exists I created a very small plugin which opens up an inventory with one item. If you click onto the item it is checking if the item you clicked on is equal to the one which was placed into the inventory, by using the equal method. It can be dowloaded from https://github.com/Simonsator/ItemDoesNotEqualItself/releases and the src code can be found here https://github.com/Simonsator/ItemDoesNotEqualItself