To reproduce:
1. Create a new project.
2. Create empty GameObject.
3. Make a prefab of it.
4. Select instance of a Prefab in Hierarchy, and add component "Rect Transform".
5. Press ctrl + z. Nothing happens.
6. Deselect GameObject. Press ctrl + z multiple times to undo "Add Rect Transform".

Expected result: pressing "ctrl + z" will always undo previous action (even if it's "Add Rect Transform").
Actual result: After pressing "ctrl + z" nothing happens if the last action was "Add Rect Transform" to an instance of a Prefab.

Reproducible: 5.4.3p1, 5.5.0p4, 5.6.0b5
Not reproducible: 5.3.7p1

Notes:
This does not affect Edit -> Undo.