Reproduction steps:
1. Open the attached "InstantiateAsyncTransformRepro.zip" project
2. Select the "Simple Data Holder" Prefab in the Project window
3. Observe the “TestList” and “TestArray” lists under “Data Holder” component
4. Open the "Scenes/SampleScene" Scene
5. Enter the Play Mode
6. Select the “Simple Data Holder (Clone)” GameObject in the Hierarchy window
7. Observe the “TestList” and “TestArray” lists under “Data Holder” component

Expected result: The elements of "TestList" and "TestArray" are identical to the "Simple Data Holder" Prefab
Actual result: All script references except for the last element are missing

Reproducible with: 2022.3.42f1, 6000.0.15f1
Couldn’t test with: 2021.3.41f1 - InstantiateAsync is not supported

Reproducible on: Ubuntu 24.04, Windows 10
Not reproducible on: No other environment tested