can you please try the following workaround mentioned in the thread vCenter Windows 6.0U3 to VCSA 6.5U1 failure .
As for me, I removed vpxd(VMware vCenter Virtual Server) as a dependency from all Windows services and migration tool successfully shutdown source machine to continue migration.
Basically, I did "sc config SERVICE_NAME depend=/" for every service that required vpxd as a parent. It messes with other dependencies the service might have, but the Windows server wouldn't be needed anyway.
-SD [vExpert 14-19,VCIX6-NV&DCV,RHCE]
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