Steps to reproduce:

1. Open attached project
2. Open scene "TestScene1"
3. Run it and press "A". This will additively add "TestScene2"
4. While still in play mode exit Unity
5. Reopen Unity and notice that both scenes are loaded although "TestScene2" was loaded in play mode

Reproduces with using both, Application.LoadLevelAdditive and SceneManager.LoadScene in additive mode.

So there are 2 workarounds:
1. Do not close the editor while in Play mode
2. If you do, remove the extra scenes when you restart the Editor

Reproduced with: 5.3.0b1, 5.3.3p1, 5.4.0b8