Steps to reproduce:

Create a new 3D URP project
Create a new UXML Document and open it (Assets > Create > UI Toolkit > UI Document)
Add a Label to its Hierarchy, and Save and Exit UI Builder
Create another UXML Document
In the Library section, navigate to the "Project" tab
Expand the "Assets" foldout and drag the previously created UXML Document into the Hierarchy
Select the TemplateContainer and rename it to anything
Once renamed, right-click and select "Open Instance in Context"
Select the Label in the Hierarchy and rename it to anything
Click Ctrl+Z twice
Observe the UI Builder and the Console

Actual results: Label disappears from the UI Builder view and "Invalid UXML or USS: System.IndexOutOfRangeException", "NullReferenceException: Object reference not set to an instance of an object" and "IndexOutOfRangeException: Index was outside the bounds of the array." errors are thrown

Expected results: Undo operation is performed with no errors

Reproducible with versions: 6000.0.75f1, 6000.3.16f1, 6000.4.8f1, 6000.5.0b9, 6000.6.0a5

Tested on (OS): Windows 11

Notes:

Reproduction can be quite inconsistent and it might be needed to repeat 7-10th steps a few times with returning from Context mode and going back