Same issue here. Seems the iPhone 5 creates video using the Apple Intermediate Codec. When playing the video in Quicktime (iMovie appears to use the QuickTime codec library to play these video clips as well) I see the exact same problem. When playing via VLC, it cannot play the video, but the autio plays and I see it suddenly jump several seconds to the end after playing for a short time.
I am also seeing the audio is mono, that is only 1 channel has any sound. Maybe that's normal and not relevant, but an observation as my other HD video camera seems to produce stero sound.
This really ***** because I didn't recognize the issue until after deleting the video clips from the iPhone, so the only copy left is the broken files stored on my Mac Pro.