To repro:

1. Open project attached
or
Create a new one, create a prefab from e.g. Cube and add several Cubes from this prefab to scene.
2. Select Cube.
3. Enter the Playmode.
4. Change Rotation (e.g. x = 45) or Position (e.g. y = 0).
5. Press Apply in Inspector (error in Console appears).
6. Exit Playmode.

Actual result: Changes are reverted. Any of instances of this prefab got changes.
Error in console:
InvalidOperationException: This cannot be used during play mode. (related case 839122).

Expected result: Changes are applied to prefab and its instances with no error.

Versions info:
There is no ability to apply changes to prefab in 5.3.6p5 (28930307ad49).
Reproducible in 5.4.1p3 (1b587b7935dc) and 5.5.0b7 (bd91e53964bc).