do you mean there are frames with dropouts on them?
you can "paint them out" using a plugin from digital heaven (only $10!)
or do you mean there are sections that never play smoothly in FCP, or going out to tape?
those shots might just be on a "bad" part of the drive, or more likely be split over more than one part: fragmented
re-captureing the shot can help.
moving the file to another drive and connecting to that can help, too.
both ways give you a new file on a new, hopefull better part of the drive.
nick