To reproduce:

1.Download and open attached project.
2.Open scene "Scene".
3.Open NewBehaviourScript.cs and uncomment the call to Test() method in Awake(line 37).
4.Enter Play mode.

Expected result: SceneManager.SetActiveScene() sets "Scene" as active scene and gameObject "Test after returning to previous scene" is created in scene "Scene".
Actual result: SceneManager.SetActiveScene() does not set "Scene" as active scene and gameObject "Test after returning to previous scene" is created in "Temporary Scene" scene.

Reproduced with: 5.6.0b5, 5.5.1f1, 5.4.3f1, 5.3.7p3

Notes: If Test() method is called from custom created editor MenuItem, everything works as expected.