Reproduction steps:
1. Open the attached “BugRepro” project
2. Open the “Assets/Scenes/SampleScene.unity“ Scene
3. Select the “Window” prefab in the Hierarchy window
4. In the Scene view, observe that the “Window” prefab is displayed with some buttons (nested prefabs) visible at the top
5. Open the “Window” prefab in context mode (click the Arrow to the right of the prefab instance)
6. Observe the Scene view

Expected result: The buttons should be visible at the top of the window
Actual result: The buttons are not visible at the top

Reproducible with: 2021.3.44f1, 2022.3.52f1, 6000.0.26f1, 6000.1.0a2

Reproducible on: Windows 11
Not reproducible on: No other environment tested

Note: Setting the sorting layer from "UI" to "Default" solves the issue