I took bio 1, bio 2, anatomy 1, anatomy 2, orgo 1, orgo 2, physics 1, physics 2, Chem 1, and Chem 2.
Just don't tell them you took it because it was easier there. I just explained that I got my AA at a community college because my scholarship covered 100% at a community college and 75% at a university and due to financial issues in my family it was best for me to go to CC. No one had a problem with it. As long as you don't have some lame excuse like "it's too hard at my university" I don't think it matters
My classes at CC were harder anyways
Edit: not to say that some schools don't prefer you take it at a university, but I don't think that puts you out of the running. I got rejected from some schools and it could be because of that but I think it's safer to assume it was my MCAT...