To reproduce:
1. Open "start" scene in the attached project.
2. Open a window: Problem -> RevertPrefab.
3. Drag "obj" from hierarchy to the obj field, in RevertPrefab window.
4. Press "revert" in RevertPrefab window.

Expected result: obj is reverted to it's prefab, but Scale is not changed.
Actual result: Scale is changed to be the same as prefab's parent.

Reproducible with: 5.6.0f1, 2017.1.2p2, 2017.2.1p1, 2017.3.0f3, 2018.1.0b1

Notes:
When "revert" is pressed, prefabs instance's position, rotation and scale is saved.
A new component is added to the Prefab parent.
Instance of a prefab is reverted.
Previously saved position, rotation and scale is set back to the Instance of a prefab.
It all works fine, only if new component is not added in the same OnGUI update.