I don't think you can debug your Matlab script from labVIEW. The following webpage talks about this:
http://digital.ni.com/public.nsf/3efedde4322fef19862567740067f3cc/19106e318c476e608625670b005bd288?OpenDocument
My suggestion would be to write a script in Matlab and thoroughly test it before calling the script from a Matlab script node in LabVIEW.