The steps to remove orphan users from Azure AD are a bit complicated, and I think the only way it can be done is from a local PowerShell session.
Here we go -
1. Install the MSOnline applet
PS C:\Users\administrator> Install-Module MSOnline
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'C:\Users\administrator\AppData\Local\PackageManagement\ProviderAssemblies'. You can also install the
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Untrusted repository
You are installing the modules from an untrusted repository. If you trust this repository, change its
InstallationPolicy value by running the Set-PSRepository cmdlet. Are you sure you want to install the modules from
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[Y] Yes [A] Yes to All [N] No [L] No to All [S] Suspend [?] Help (default is "N"): Y
2. Connect to the MSOnline service
PS C:\Users\administrator> Connect-MsolService
3. Remove users one by one
PS C:\Users\administrator> Remove-MsolUser -UserPrincipalName my-user@my-domain.com
Confirm
Continue with this operation?
[Y] Yes [N] No [S] Suspend [?] Help (default is "Y"):