To reproduce this bug:

1. Import the attached package
2. Open 'Test' scene
3. It has 4 empty gameObjects and script with array of Transforms, printing out in console OnDestroy() whether they are equal to null or not
4. Press play and stop the scene
5. You get inconsistent and random results in the console
6. Sometimes it is possible that all the results be true or false

By Design: Destroy() does not guarantee any ordering. You can use DestroyImmediate() instead