Hi @edward33,
This is a limitation of the clone_items() method and Experience Builder items are not supported with it at the moment.
From what I've seen, both versions of ArcGIS Online Assistant also cannot properly copy an Experience Builder app. While the item for the Experience is cloned in the target organization, the copy of the app still references the maps, apps, and other underlying layers used in the original Experience, as this workflow (similar to the Python API clone_items() method) only copy the app item and not other items that are used in this app in different ways or forms.
Until this functionality is added to ArcGIS API for Python in future releases, one possible workaround is to clone Web Maps and/or Feature Services and/or apps used in the Experience using clone_items() method, and then rebuild the Experience Builder app in the target organization.
Best,
MJ