When you set velocity value to any vector3, it only changes after few frames, not instantly.

1. Open project "Test"
2. Open scene "Test"
3. Play
4. Move object "GameObject" in the scene, "Capsule" going to follow it
5. Click button in the centre of screen "Button", it outputs "Capsule" velocity, then changes it to zero and outputs it again
6. In console you get something like this, for exmaple:
(0.0, 0.0, 1.2)
(0.0, 0.0, 1.2)
But you should get:
(0.0, 0.0, 1.2)
(0.0, 0.0, 0.0)

Reproduced: 4.6.0f1, 5.0.b13, 5.0.b16