Reproduction steps:
1. Open the "1368465.zip" project
2. Open the "SampleScene" Scene
3. Drag and drop the "MyPrefab" Prefab into the Scene on one end of the "Cube" Game Object
4. Observe the inserted Prefab's Y Position value in the Inspector window
5. Drag and drop the "MyPrefab" Prefab into the Scene on the other end of the "Cube" Game Object
6. Observe the inserted Prefab's Y Position value in the Inspector window

Expected result: Both Prefabs have Position Y value equal to 0
Actual result: One Prefab has Position Y value equal to ~0.0009492569

Reproducible with: 5.0.3 (2019.4.31f1, 2020.3.22f1, 2021.2.2f1), 5.0.4 (2022.1.0a13)