Hi Shujaath,
To narrow down the issue, I'd like to confirm the following information:
1. Are you using multiple filtering methods to sync users?
2. Are the unexpected user with the verified domain suffix or a local domain suffix?
Considering the current situation, please refer to the following steps to troubleshoot the issue.
1. Make sure that only one filtering method is being used at the same time.
2. Manage Windows Azure AD using Windows PowerShell.
3. Run the cmdlet: Remove-MsolUser -UserPrincipalName user@domain.com.
4. Force directory synchronization. After that, check whether the user user@domain.com is restored at Office 365 side automatically.
Best Regards,
Bruce Zhou