Teams should use the username in Azure AD. Azure AD controls access to Teams, as well as all your other Office 365 applications. If the users are internal and part of your organisation, the login should typically be email@example.com. If you have guests in Teams then they may be other logins such @Hotmail.com, @Gmail.com etc.
Can you describe in more detail? Is what is in Azure AD for them something completely different from what they are logging into Teams with?