I have seen issues with the incorrect UPN configuration on premises causing problems like this. For example, the user name may not be the same as email address and the UPN for the user may have a different suffix than the custom domain.
Can you check the name for the user you are trying to authenticate with? Since you are using pass-through authentication users credentials are verified on your on-premises environment when they try to sign in.
Open a PowerShell as an administrator
Run the PowerShell cmdlet “Connect-MsolService”
Run the PowerShell cmdlet “Set-MsolDirSyncFeature -Feature SynchronizeUpnForManagedUsers -Enable $true”
Run full synchronization using the PowerShell cmdlet “Start-ADSyncSyncCycle -PolicyType Initial
Check whether the UPN has changed.
If it has not changed, use:
Set-MsolUserPrincipalName -UserPrincipalName xxxxxxxxxxx -NewUserPrincipalName yyyyyyyyyyy`
In the troubleshooting guide, see the section for users get invalid username/password error