My hunch is that they would understand. Your major didn't require those courses, so when you had to take them to prep for your master's program, you just took them at the local community college. I don't see why that would be a problem, since they know you're just doing it to take care of pre-reqs.
That being said, I would do everything I could to make sure my grades were perfect in any community college courses I took! This is again just a hunch, but I would bet that they don't view a 'B' in calc 1 from Joe the Plumber Community College as being equivalent to a 'B' in calc 1 from MIT.
Best of luck!
~possible_phd the applicant, whose opinions are just his best guesses and are in no way guaranteed to be accurate