Is it OK to exclude 'extra courses' from the GPA reported in my CV?
If you write 


  GPA: 3.5


in your CV, this implies that your official cumulative GPA as per university records is a 3.5. So to write this is misleading, and unethical.

If you want to list your GPA only for courses in your own department, you can write


  Major GPA: 3.5


or 


  3.5 GPA in physical science courses