[Demonstration 1]

[Buggy Method]
@Override
public ItemStack getCraftingResult(InventoryCrafting inventoryCrafting) {
    int energy = 0;
    IEnergyTool energyTool = (IEnergyTool) getRecipeOutput().getItem();
    for (int slot = 0; slot < inventoryCrafting.getSizeInventory(); slot++) {
        if (inventoryCrafting.getStackInSlot(slot) != null) {
            ItemStack stack = inventoryCrafting.getStackInSlot(slot);
            if (stack.getItem() instanceof IEnergyContainerItem) {
                energy += ((IEnergyContainerItem) stack.getItem()).getEnergyStored(stack);
            }
        }
    }
    return energyTool.setEnergy(getRecipeOutput(), energy);
}

[Buggy Hunk]
return energyTool.setEnergy(getRecipeOutput(), energy);

[Patch]
return energyTool.setEnergy(getRecipeOutput().copy(), energy).copy(); //might be redundant but in my experience a spare .copy() never hurts

[Demonstration 2]

[Buggy Method]
@Override
public SPacketUpdateTileEntity getUpdatePacket() {
    NBTTagCompound tag = new NBTTagCompound();
    writeToNBT(tag);
    return new SPacketUpdateTileEntity(this.pos, 0, tag);
}

[Buggy Hunk]
return new SPacketUpdateTileEntity(this.pos,0,tag);

[Patch]
return new SPacketUpdateTileEntity(this.pos,1,tag);