This has only really happened to me on larger vessels. I had assumed it was either due to clipped parts or just a limitation in Squad's latter revisions of the SAS function. Not had the problem since I installed Kerbal Joint Reinforcement.
Your example is interesting, however, in that the vessel looks like it has very few parts AND it looks like it's also occurring during time warp.
...gotta say, my first suspicion would be that PhysicsRangeExtender!
If that doesn't solve it, try taking a backup of your save game, then continually remove half of your mods until you identify a cause.
TMS's post in Ship Jitter/Shaking was marked as the answer