My model contains Simulink inport and output blocks at the top level which are used in data import and export for the simulation. However, when I simulate this model with System Generator blocks, I receive a "Fatal Internal Error" message.
This is due to a known compatibility issue with this type of simulation flow. Simulink inport and outport blocks at the top level of the model cannot currently be supported with System Generator designs.
An alternative to this is to use "To Workspace" and "From Workspace" Simulink blocks which can be used in much the same way to bring in variables from the MATLAB workspace, and capture simulation results to new workspace variables.
This issue is resolved in 11.3.