This was caused by a previous migration from On Demand to in-house. There were duplicate entries for some of the users as a result of the internal Confluence directory (thanks RJ). I was able to resolve this by simply disabling the Confluence user directory. For anyone with the same issue unable to disable the Confluence directory, you should be able to temporarily disable JIRA directory and then delete the bad Confluence accounts.
My assumption in this case is that the Confluence users license count is pulling not only JIRA users but other users also.
If you have other users directories besides JIRA one like the internal directory or a LDAP directory, you may need to verify if they aren't counting different users to your license. Probably they are.
Hope that helps :)
Most probably there's some users in your Internal Confluence directory. Perhaps you could double check on that, as Confluence will take all the users that have 'Can Use' permission, and will count it towards the license. You could disable the users that is not in used anymore in Confluence Admin >> Users. For more information please refer to the following.
Hope it helps.
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