The rootVisualElement of a UIDocument component is recreated after MonoBehaviour.Start() is invoked. 
The problem is that MonoBehaviours that uses the content of this UIDocument 's rootVisualElement are left with references to the old rootVisualElement.

Steps:
1. Create a Scene
2. Add a new UIDocument using "Assets/UI Toolkit/UI Document" menu item
3. Set the source asset of the UIDocument to an valid uxml asset with a button.
4. Create a MonoBehaviour and add it to the UIDocument game object.
5. In Start() of the MonoBehaviour, connect an action to the click event of the button of the UIDocument.

void Start()    

{

           getComponent<UIDocument>().rootVisualElement.Q<Button>().clicked += myAction;        

}

6. Open the UI Builder
7. Start play mode
8. Verify that clicking on the button triggers your action.

Actual outcome:
The action is not executed because the whole UI Document's content has been recreated with a new rootVisualElement after Start() was invoked (seems to be caused by due to live update).

Expected outcome:
Not sure,
1) Maybe the content should never been recreated
2) or there should be at least a notification when the content is recreated but this lead to a different way to access with UIDocument from MonoBehaviours.