ESXi hosts and VMs with Windows Server guest OS have completely two different upgrading methods ... When you upgraded the host, did you upgrade the hardware compatibility of those VMs or not? (before upgrading the VMware tools)
Instead of windows log, please check the vmware.log file in the VM directory path inside the datastore, especially time duration of upgrade actionsPlease mark my comment as the Correct Answer if this solution resolved your problem
Why are you not going for direct upgrade of ESXi to 6.5 instead of current version -> 6.0 -> 6.5 ?
Since you are ESXi upgrade in latter way, you will have to upgrade VM hardware version upgrade in same way as well. Like this: Current version -> 11 -> 13. So double downtime per VM.
Also, what NIC are the VMs using ? VMXNet should be there instead of E1000 unless there's a particular reason.
What are your observations on the VMs which are facing the issue ? Any common pattern you observed; like same OS, or NIC or host or cluster ?