Steps to repro:

1. Open attached project;
2. Open Assets -> Scenes -> main.unity;
3. In the Hierarchy expand UI -> Main Window;
4. Delete 'Button' gameobject from Hierarchy (should be highlighted in blue);
5. Drag and drop 'Button' prefab from Assets -> Scenes to Hierarchy;
6. Open Edit context menu and Undo several times.

Actual result:
Unity crashes. See attached video.

Last calls from the stacktrace:
0x00000001411B8DEA (Unity) UI::RectTransform::UpdatePosAndRect
0x00000001411C0526 (Unity) UI::RectTransform::UpdatePosAndRectRecursive
0x00000001411C0624 (Unity) UI::RectTransform::UpdatePosAndRectRecursive
0x00000001411C0624 (Unity) UI::RectTransform::UpdatePosAndRectRecursive
0x00000001411C3A83 (Unity) UI::RectTransform::SetSizeDelta
0x00000001418FA94B (Unity) UI::Canvas::UpdateCanvasRectTransform
0x00000001418FAC9D (Unity) UI::Canvas::SetScaleFactor

Expected result:
Unity should not crash. Deleted prefab instance should be restored in Hierarchy panel.

Notes:
- Reproducible in 5.6.0b6;
- Was unable to reproduce in previous versions, since Editor crashes when opening project from previous versions;
- Was unable to repro from scratch; seems to be related to the current project;
- Reproducible on Windows 10 and OSX 10.12.2.