sharepoint review scope

what would be some useful checks to include in an audit/health check of SharePoint (and document management in general). The obvious one we can think of is around permissions of documents stored in SharePoint, to ensure sensitive documents are only accessible by the approved users/groups - but I wanted to spread the review a but further, and was hoping for some inspiration on what above and beyond security permissions would be useful when looking at such a system (it doesn't have to all be about security). Any common SharePoint mistakes/risks above and beyond permissions also most useful,
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