Hi Giorgia,
My apologies for the delay in responding. I noticed that by deleting and re-adding the emissions branches under Household\Water Heating demands, the problem was fixed.
Also, I am not sure if you need to have emission factors for the fuels in the Transformation\...\Output Fuel branches since you have already specified emissions factors for these same fuels under the demand branches. You are essentially double counting the emissions since the fuels produced by the transformation modules are used by the demand branches.
Hopefully this helps,
Emily