How to reproduce:
1. Open the attached project
2. Open and play Test scene
3. Click on Die button (lizard will play Die animation)
4. Select lizard in Hierarchy
5. Click Apply on prefab in Inspector
6. You will get an error: InvalidOperationException: This cannot be used during play mode.
7. Disable play mode
Result: The changes of position and whole model you tried to apply are applied the the prefab

Reproducible: 5.4.4p1, 5.5.1p1, 5.6.0b5
Not reproducible: 5.3.7p3 (Apply and other buttons disappeared on play mode)

Fixed: no error and changes are applied