The error message
Some users (*) have over 5000 items which is over SharePoint List View Threshold limit is displayed in the User Report.
This issue occurs because SharePoint Online uses the Large List Resource Throttling feature. By default, the list view threshold is configured at 5,000 items. When the defined item limit in a list is exceeded, the message is displayed.
Firstly, the items will still be migrated, but they won't be displayed. They can only be accessed via search. You will need to index and sort the items in Sharepoint.
Please refer to this Microsoft article for more information on managing large lists and libraries.