No application to medical school (or residency) is perfect, which is why it's important you have a well-considered strategy for managing interview questions about gaps in your candidacy. Addressing a bumpy freshman year or a suboptimal first MCAT attempt with aplomb can make a big difference in how an interviewer and admissions committee perceives you.
Check out this KevinMD article I wrote a few years back that specifically addresses how to be upfront about a major deficiency in your candidacy and how to demonstrate — with evidence from the remainder of your application — that the weakness is not representative of your abilities.