We have selected more than one facility type in sipfacilitytype, but as we cannot separate consumption between the two, why do the subsequent questions and tables in both energy and water sections indicate only one of the facility types entered?

This is not a technical error, moving forward from FEM 4.0 the expectation is that facilities put things in place to be able to report on energy and water consumption separately, by facility type. 

If you answered "yes" to the question "Is your facility able to separately report energy consumption by each facility type?", you would find the relevant distribution on the assessment to be able to enter the data between the two facility types, however, so long as you answer "no" to this question, even if your data input corresponds to the combined facilities, the assessment will indicate only the first facility type input on the sites and permits section. 

It is designed this way to encourage facilities to put things in place as soon as possible to split out their reporting and tracking accordingly so that combined figures are not entered into one place.