How to reproduce:
1. Create a new 3D project
2. Create 2 new scenes - “ReproScene” and “EmptyScene”
3. Load “ReproScene” and create an empty GameObject
4. In Hierarchy select the newly created GameObject and copy it (ctrl + c)
5. Paste the GameObject at least 5 times (ctrl + v)
6. Undo until all empty GameObjects disappear from Hierarchy (ctrl + z)
7. Redo until all empty GameObjects appear in Hierarchy (ctrl + y)
8. Save “ReproScene” and open “EmptyScene”
9. Re-open “ReproScene”
10. Repeat steps 3-9 at least 2 times

Expected result: the scene with empty GameObjects is loaded without any errors
Actual result: the scene with empty GameObjects loads but some GameObjects have corrupt transforms

Reproduced with: 2021.3.11f1, 2021.3.14f1
Not reproduced with: 2020.3.46f1, 2021.3.10f1, 2021.3.21f1, 2022.2.12f1, 2023.1.0b8, 2023.2.0a7
Fixed in: 2021.3.15f1

Reproduced on: Windows 10 (by reporter), Windows 11

Errors logged in Unity Editor:
1. Problem detected while opening the Scene file: 'Assets/Scenes/SampleScene.unity'. Check the following logs for more details.
2. Found a Transform component that is not assigned to a GameObject. A new GameObject 'Recovery GameObject for Transform (ID in file: 935452317)' has been created to contain the component.
3. Found a Transform component that is not assigned to a GameObject. A new GameObject 'Recovery GameObject for Transform (ID in file: 351552028)' has been created to contain the component.

Notes:
1. Reproducible without shortcuts (Right-Click on GameObject > Copy > Right Click in Hierarchy > Paste; Edit > Undo History > Undo > Redo)
2. Shortcuts can be found in Edit > Shortcuts. Refer to Unity documentation: https://docs.unity3d.com/Manual/UnityHotkeys.html
3. Reproducible when saving scene in versions 2021.3.11f1, 2021.3.12f1, 2021.3.13f1, 2021.3.14f1 and opening in any other version