Why are the counts for Portal for ArcGIS Index Status more than the actual total items on the portal?

The Portal Administrator Directory Index Status shows the items count as 13000+ and groups as 500+, but the actual values in the portal don't have that many items, groups and users. 

This issue is related to a known limitation with the software.

The raw indexer values in the index status include several internal users, items, and groups that are created as part of a fresh installation. As a result, the numbers reported by the indexer cannot be directly compared to the content visible in the Portal UI. This is why it is expected to see higher counts in the index status compared to what is shown in Portal.

For reference, review the following documentation:

• Bug: Portal for ArcGIS index status for users, 'Count in store', reports more than the actual total named user accounts created with the portal Home application
• ArcGIS REST APIs: Status - Indexer
• Esri Community: What is a Portal search index item?