Translucent materials appear in all stencil layers when rendered in the Movie Render Queue

No matter how many passes there are translucent objects will appear in all of them. A notable case is particles, as their materials are often translucent. Using masked materials is a possible workaround.

1. Create a new level sequence.
2. Add a cube to the sequence
3. Edit the material on the cube, and set its blend mode to translucent
4. Add a camera and camera cut track by pressing the camera button in the sequencer toolbar
5. Move the camera to have vision of the cube
6. Add the cube to a layer
7. Open the movie render queue
8. Add a job for the created sequence
9. In the Deferred Renderer settings add a stencil layer for the cube
10. Check "Add Default Layer"
11. Check "Accumulation Includes Alpha"
12. Accept the settings and render the sequence 

RESULT

The cube appears in all passes