I have the same issue when using the EN15804-A2 impact assessment method.
However, after running many many analysis of processes in EcoInvent using this method, i have never gotten any results on the EE impact category.
I have personally dealt with this, by making 00's in all cells related to EE, unless there was a clear export of energy in those life cycle stages (sale of energy from solar cells, residual heat from production transfered to district heating, etc.).
This method has gotten third party verified in the EPDs i have made, even though it may not be scientifically rigorous.
I hope this helps,