During the Certificate Swap, customer noticed that intermediate certificate thumbprint is populating as secondary certificate, which cause the cluster upgrade operation to fail.
This is a known issue with the AzureRM ServiceFabric powershell CmdLet, which fixed in latest AzureRM.ServiceFabric 0.3.3(To upgrade, please run Install-Module -Name AzureRM.ServiceFabric -Force). However if the rolling is completed, please suggest the customer to update the certificate manually from resource explorer.