How to reproduce:
1. Open user-submitted project (ReproPrefabComponentOrderBug.zip)
2. Open the ReproScene
3. Open 'RootPrefab' GameObject in Prefab Mode
4. Select 'NestedPrefab' GameObject, right-click the Animator Component and select 'Move Up'
5. Save the changes to the Prefab and exit Prefab Mode
6. Select 'NestedPrefab' and see the Component order

Expected result: the Animator is above the Box Collider
Actual result: the Animator remains below the Box Collider

Reproducible with: 2018.4.27f1, 2019.4.10f1, 2020.1.5f1, 2020.2.0b2

Notes:
The same behavior can be observed by opening the RootPrefab, removing both Components from the NestedPrefab, saving, re-entering Prefab Mode and adding Animator first and Box Collider second; after saving and exiting Prefab Mode the Animator will be moved to the bottom