One consume inside the logic:

https://github.com/Jozufozu/ExNihiloOmnia/blob/master/src/main/java/exnihiloomnia/blocks/barrels/states/compost/logic/CompostStateLogicItems.java#L44
which calls
https://github.com/Jozufozu/ExNihiloOmnia/blob/master/src/main/java/exnihiloomnia/blocks/barrels/architecture/BarrelLogic.java#L28

and the other inside the insertion method:
https://github.com/Jozufozu/ExNihiloOmnia/blob/master/src/main/java/exnihiloomnia/blocks/barrels/tileentity/TileEntityBarrel.java#L164

Not completely fixed - I have 2 barrels in which I insert with EIO conduits. Each barrel should accept 8 leave blocks (tested by manually inserting with right click).

After the fix it now consumes 9 leave blocks. Using the speed downgrade (which only transfers single items) fixes this too.

So i assume somewhere on the state transition is another consumeItem.