Reproduction steps:
1. Open the attached “ReproProj”
2. Open “Assets/Scenes/SampleScene.unity“ Scene
3. Double-click the “GameObject2” Prefab in Project view
4. Exit Prefab view

Expected result: Cube in Scene view looks as in step 2
Actual result: Error “A BatchDrawCommand was submitted with an invalid Batch, Mesh, or Material ID. This is not supported when rendering with a BatchRendererGroup or anything based on it like GPU Resident Drawer or Entities Graphics.“ is present

Reproducible with: 6000.3.0b10 (9f756a58f7c9)
Not reproducible with: 6000.0.62f1, 6000.2.13f1, 6000.4.0a5
Fixed in: 6000.3.0f1 (820bc0c5f094)

Testing environment: Windows 10 Enterprise 21H2
Not reproducible on: No other environment tested