To reproduce:

1. Open attached project.
2. Run editor test: GetRootGameObjects_AfterSceneMerge_DestinationHaveBothSceneRoots with double clicking on one of them.
3. Run the same test again, when it asks to save scenes, press "Don't save scene"

Expected result: Test runs fine.
Actual result: Test Runner dialog does not disappear and error is thrown:

ArgumentException: Invalid SceneManagerSetup:
Scene: 'Assets/Temp/TempScene.unity' doesn't exist.
No loaded scene found.
One active scene is required. Number of active scenes: 0

The test itself creates some scenes and then merges them. Maybe it is related how the framework deals/remove/cleans the scenes before running test (?)

Reproducible on:
Version 5.6.0b5 (802d0eaaa43c)
Sun, 15 Jan 2017 18:38:47 GMT
Branch: trunk