This 

warning will occur for partitions between 2 merged zones. Because of the merging, the zone is the same on both sides of the partition and EnergyPlus flags this as a potential mistake. To avoid this message, you can select the 'Surfaces within zone treated as adiabatic' model option for Heating design, Cooling design and Simulation calculation options. In this case such partitions will instead be modelled using an adiabatic formulation where the Outside face environment surface is the same as the actual surface and the warning is not generated.

The warning can in any case be safely ignored.