Often happen that a customer has more then one email domain in his On-Premises infrastructure. This should be considered when you plan to deploy AD FS Services to enable Single Sign-On with Office 365.
With the newest version of Azure AD Connect, steps to federate On Premises AD DS with Azure AD is fully automated though it assumes that the domain specified during the wizard steps is the only one domain you want to federate (If you need an overview of Azure AD Connect step-by-step configuration, please refer to Microsoft Docs here).
This will cause disruption of users login to Office 365 apps. To solve this situation you need to change the federation mode configured by the wizard manually using Powershell and set it to a Multi Domain federation. Read More