The following error is present in the ADC.wlog file:
2018-08-31 07:43:20,581 [274] ERROR PowerShellHelper - Failed to Execute cmdlet: Get-Mailbox -ResultSize unlimited -Verbose -OrganizationalUnit OU=company.onmicrosoft.com,OU=Microsoft Exchange Hosted -RecipientTypeDetails SharedMailbox | SELECT ExternalDirectoryObjectId, Name, ServerLegacyDN, LegacyExchangeDN, OrganizationalUnit, EmailAddresses, PrimarySmtpAddress, IsValid, IsMailboxEnabled, Guid
1. Run Get-OrganizationalUnit -ResultSize unlimited and note the correct OU.
2. Specify the correct location of where your mailboxes are in Azure AD in the Organizational Unit field under Advanced Configuration of the Azure AD Connector
RESOLUTION 2
Leave the Organizational Unit Field blank on the Advanced Configuration page. When Get-Mailbox is ran by the Azure Active Directory Connector it will retrieve information about all mailboxes in Office 365.