Users are being duplicated in the People directory each time Confluence is restarted, until a re-index is performed (at which time the duplicates are removed).

If you encounter a bug where your people directory is displaying duplicates and this isn't fixed by performing a re-index, it's likely that you're affected by CONF-30050.

Please take a look at this Knowledge Base article for more information:
https://confluence.atlassian.com/display/CONFKB/Duplicates+in+the+People+Directory

Workaround

Step 1. Rebuild the search index to remove the duplicates in the people directory.
Step 2. Perform an action that will add a different type of indexing task to the queue before your instance is restarted - e.g. create a page in Confluence.

If this doesn't work for you, please raise a support ticket so that we can investigate further.