I had 1-3 outstanding for most of the schools I applied to and they didn't seem to care much as long as I would have them done and I had a plan for how to do that by the spring semester. Some schools like Davis, UTenn and FL said that I could even have the summer to finish them (which was nice because then I could take only the one I ended up needing instead of the 5 or 6 (bc they didn't all overlap requirements). On the other hand, Ohio wanted me to have the 2 I still needed done in the Spring (which I couldn't fit in my schedule/didn't want to overload because I was working too) so I had to withdraw my application and I couldn't apply to Western because there were too many pre-reqs I didn't have.
So really, it totally depends on the school, but it doesn't usually seem to be a problem esp if you are taking them in the spring.