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.