Issue description

There is a known issue with the OneDrive usage in the Microsoft 365 center, count from all libraries within the site collection. There can be files in system libraries e.g. _catalogs which will be included in this count. That’s why the files count does match with the amount of the files the user has in the root folder library

Latest updates and guidance:

This is being investigated by Microsoft under 31732567.

Microsoft have provided the following KB article and will be updating it to reflect the known issue in the month of July:
Microsoft KB article