Hi @Natan1881 ,
Agree with Andy that it's an expected behavior that the items count returned by the Get-MailboxFolderStatistics cmdlet is different with what are visible to the users. This is because the output returned by the cmdlet also includes hidden items. To add to the link shared by Andy, you can also check the link below which applies to Exchange 2013:
Get-MailboxFolderStatistics
You run the Get-MailboxFolderStatistics cmdlet for other mailboxes as well to verify this.
If you still have concern on this given the information above, I'd suggest confirming if the users have any idea about the missing messages, like if they are all old messages prior to a certain date. Feel free to post back should you need further assistance on this.
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