I have experienced it a few times, and at first instance it is alarming. However relaxing into it helps. Your brain and body eventually sync up again.
What does however happen to me almost nightly is a hypnagogic reflex. That is again where the body and brain fall slightly out of sync, except when you are starting to fall asleep. You may already be drifting into a dream state, but the mind still hasn't shut down it's motor controls yet, and you might all of a sudden find yourself jerking awake.
The upside is, you can take advantage of this to slip into lucid dreaming. =)