The NavMeshes in different Scenes are not connect by default. When you load another level using Application.LoadLevelAdditive() you will need to connect the NavMeshes in different Scenes using an Off-Mesh link.
In this example we have Scene 1 and Scene 2. The Scene 1 has an Off-Mesh Link starting over a walkable area and landing over a walkable area in Scene 2. There can be as many Off-Mesh Links connecting the Scenes as necessary.
When authored the other end point of the scene connecting Off-Mesh links are not connected. After a new Scene is loaded, the Off-Mesh Links will be reconnected.
If the multiple scenes have NavMesh overlapping at the same area, the position picking may be arbitrary NavMesh at that ___location. This applies to agents, Off-Mesh Links and position picking using the NavMesh API. You should create the scene crossing Off-Mesh links so that they start and end clearly on over one NavMesh only. Overlapping NavMesh areas are not automatically connected.