From the manual:
The Physics behavior simulates physics separately to the Construct 2 layout. Construct 2 will try to keep the Physics and Construct 2 "worlds" synchronised if one changes but not the other, but this can be unpredictable. For example, setting an object's position or angle will cause Construct 2 to teleport the corresponding object in the physics simulation to the object's new position, which does not always properly take in to account collisions. The same is true of using other Construct 2 behaviors at the same time as Physics.
Therefore it is highly recommended to control Physics objects entirely via the Physics behavior (by setting forces, impulses, torques etc.), rather than trying to manipulate objects by Set position, Set angle etc.
It's always unpredictable when you move physics objects without using the physics actions.
You could use a separate sprite for aiming and then spawn the missile when you're ready to launch. physicsPin.capx (r102)
Or the other option would be to rotate it with 'set torque' instead of pinning it.