Coming out of timewarp in the sphere of influence of Mun or Minmus, the craft slows down. I didn't do too much testing with the bug, testing edge cases and stuff like that, but here is what I do remember:
-enter timewarp, everything looks fine. pull out of timewarp, you lose a couple meters per second.
-The slowdown is always retrograde, regardless of which way the ship is pointed in 3d space. whether you're coming in nose first or legs first, it is always retrograde.
-this applies if i've landed, run timewarp while on surface, then come out of timewarp while still on surface, then launch, then do more timewarp shenangans, bug still occurs.
-wonder what happens if u separate a ship while in mun SoI, creating a new entity, then mess with timewarp. i dont know what happens there.