They told me a similar thing before they had even see my application because I took the MCAT and sent in AMCAS before completeing all of my pre-med requirements.
Out of curiousity, are you in the same boat? Most schools don't seem to care, as long as you did OK on the MCAT, although Cornell is very explicit about you having to have completed all the reqs. by January of the year you are applying. I will still have a semester to do at that point, so I didn't bother applying to Cornell--their loss, of an application fee if nothing else.
This shouldn't hurt you, as met19 points out, since Downstate has as late of a rolling addmssions process as any school I know of. I think the ADCOM consideres first-time applicants (as opposed to people on the wait list) well into April or so.
