What is the TYPO3 reference index and why can it contain outdated values?
The reference index is a table with all relations between records. For example, if you place a content element on a page it also creates an entry in the reference table which keeps track of the relation between the tt_content record and the pages record.
The only thing it is used for is to show how many references there are to a record and which records have references to it in the backend. Also this is used to display a warning if you try to delete a record with references.
It can contain outdated values for various reasons. In the backend the reference table is (mostly) updated automatically, but any extension that adds or removes records not using the standard backend methods might not update it. You could for example have an extension which creates records through the frontend. These usually don't update the reference table. (Extbase supports the updateReferenceIndex option for this.)
Also, if any errors occur when adding, editing or deleting something, even using the standard backend ways, the reference index might not be updated properly.