Reproduction steps:
1. Open the attached “IN-92082” project
2. Open the Preferences window (Edit > Preferences)
3. Under “Entities” Tab, make sure “Scene View Mode” is set to “Runtime Data”
4. Open the “Scenes/SampleScene” Scene
5. Enter the Play Mode
6. Select the “Cube” GameObject from the Subscene
7. Observe the Transform controls in the Scene View

Expected result: Transform controls move along with the GameObject
Actual result: Transform controls stay in the same place and, when used, teleport the GameObject to that position

Reproducible with: 2022.3.55f1, 6000.0.34f1, 6000.1.0b1
Couldn’t test with: 2021.3.45f1 - No support for “Entities” package

Reproducible on: Windows 10, Ubuntu 24.04, Ubuntu 24.10 (user)
Not reproducible on: No other environments tested