There are a few instances on the following class that it is calling Ingredient#getItems and at some point calling SoulBoundUtils#getBoundIfCapable which is able to modify the itemstack, causing incompatibility with mod AllTheLeaks

https://github.com/Team-EnderIO/EnderIO/blob/aeef317885875e2eb02f208086c39db4273c709e/enderio/src/main/java/com/enderio/enderio/compat/jei/extension/ShapedEntityStorageCategoryExtension.java

https://gnomebot.dev/paste/mclogs/WRjdCle#L9782