Reproduction steps:
1. Create new project.
2. Create new gameobject.
3. Drag it to project window to create prefab.
4. Add rect transform component to created prefab.
5. Press undo till undo "Create/Replace prefab" triggers.

Expected result: Prefab will be destroyed.
Actual result: Error appears: "GameObject has multiple Transform components! Merged into single one."

Note: Unity will crash if you press redo "Create/Replace prefab"

Reproduced on: 5.3.6f1, 5.4.5p2, 5.5.3p3, 5.6.1p1, 2017.1.0b6.