Yeah, this could get very messy. A few people I know had to retake a couple of core rotations; they now have to graduate late (some rotations last 3 months). Assuming you''ll avoid that scenario, aside from the important points Dr. Cox mentions, I found (MS-IV last year) it was really time consuming to apply and make sure *everything* gets in at the right time. Plus, your grades and dean's letter may be delayed.
It can be tough to schedule 4th year rotations at the beginning of the year. At my institution, peds was popular, and within one day all the pedi electives for the beginning of the year were snatched. So if one of your delayed rotations becomes your fave, you may get squeezed out of a good elective.