You can use Powershell to verify see whether the user comes from "Windows Server AD" or "Azure Active Directory."
Run:
Get-AzureADUser -All $true
(You can also filter on other attributes, of course.)
To get cloud-only users you can run:
Get-AzureADUser | Where {$_.DirSyncEnabled -ne $true}
In the portal you can check the Directory synced, Creation type, and Identity issuer columns.