You can debug the generated mex and identify the problem site. To debug generated MEX code, just pass the -g option to codegen and that will compile a debug MEX file. You can then debug that MEX code by following the same process you'd use for debugging hand-written MEX files:
In short, you compile and run the MEX in MATLAB and attach Visual Studio to MATLAB, stopping when the MEX code is executed.
Note that the -g option is the same as the Coder config setting EnableDebugging:
