Most people apply during the year prior to pharma school matriculation. So you'd have Fall & Spring semesters to continue your prereqs prior to starting. I think the majority of applicants probably still have a class or two to finish. I don't think it's a big deal - probably the norm - although it is helpful to have taken some of the harder prereqs (O Chem, micro, and A&P are usually considered the big ones) so you can show you can handle the coursework.
Don't sweat it.