Yes, for Quartus® II software versions 11.1 and later, the UniPHY EMIF toolkit is not compatible with SOPC builder projects. This is due to a change in the debug architecture.
Device Family: Arria® II GZ, Arria® V GX, Cyclone® V E, Stratix® III, Stratix® IV E, Stratix® V E
Area: Component, EMIF
If you require to use the UniPHY EMIF toolkit and have an SOPC builder project in Quartus II 11.1 or later, some options are :-
Convert the project to use Qsys instead of SOPC builder
As a starting point, debug the External Memory Interface using the standalone example design project that can be generated with the UniPHY IP using the Megawizard flow.
Not recommended, but you could generate the SOPC builder project in an earlier Quartus II release than 11.1 and use the EMIF toolkit for that Quartus II software version.