To reproduce:
1) Select PrefabEditPanel
2) Click "Create Prefab Instance" button two or more times. A prefab is added to Contents with each click.
3) Select the text object of one of the prefab instances and change the text value
4) Click "Apply" to change the SampleTextPrefab

Expected result: The prefab should be updated and all instances should change to the new text.
Actual result: Unity generates the following error messages in the log file and then crashes.

Prefab has multiple Transform components! Removing them automatically would not be safe.
UnityEditor.PrefabUtility:ReplacePrefab(GameObject, Object, ReplacePrefabOptions)

Assertion failed on expression: 'rootTransform != NULL'
UnityEditor.PrefabUtility:ReplacePrefab(GameObject, Object, ReplacePrefabOptions)

MissingReferenceException: The object of type 'RectTransform' has been destroyed but you are still trying to access it.
Your script should either check if it is null or you should not destroy the object.
at (wrapper managed-to-native) UnityEngine.Component:get_gameObject ()
at UnityEngine.Component.GetComponentsInParent[RectMask2D] (Boolean includeInactive, System.Collections.Generic.List`1 results) [0x00002] in C:\buildslave\unity\build\artifacts\generated\common\runtime\ComponentBindings.gen.cs:142
at UnityEngine.UI.MaskUtilities.GetRectMaskForClippable (IClippable clippable) [0x00017] in C:\buildslave\unity\build\Extensions\guisystem\UnityEngine.UI\UI\Core\MaskUtilities.cs:114
at UnityEngine.UI.MaskableGraphic.UpdateClipParent () [0x00018] in C:\buildslave\unity\build\Extensions\guisystem\UnityEngine.UI\UI\Core\MaskableGraphic.cs:203
at UnityEngine.UI.MaskableGraphic.OnEnable () [0x0000f] in C:\buildslave\unity\build\Extensions\guisystem\UnityEngine.UI\UI\Core\MaskableGraphic.cs:122
UnityEditor.PrefabUtility:ReplacePrefab(GameObject, Object, ReplacePrefabOptions)

Reproducible: 5.5.0b1, 5.5.0f3, 5.6.0a6
Not reproducible with 5.4.3p2
Regression introduced in 5.5