To reproduce:
1. Open attached project "UnloadSceneAsyncBug"
2. Open "loaderWorking" scene and Play it.
3. Press "SCENE 1" button in Game window. "loaderWorking" scene is destroyed, because we waited 1 frame.
4. Stop Play mode.
5. Open "loader" scene and Play it.
6. In Game window press "SCENE 1" button. Loader scene is not unloaded.

Expected result: When new scene is loaded asynchronously, other scene can be unloaded.
Actual result: After new scene is loaded asynchronously, previous scene can be unloaded only in the next frame.

Reproducible with: 5.4.4p4, 5.5.1p3, 5.6.0b10

Workaround:
Wait one frame to unload scene.

Notes:
It happens because Unity thinks, that scene which we try to unload is still the only scene.