if you can repro the issue then, try to disable xcopy on the host and then retry to perform storage vmotion of the ubuntu vm and provide feedback.
The reported issue points to an underlying storage corruption on vm disk post storage migration.
there are multiple factors and variable that could be involved.
PS: please clarify if both VMFS5 & VMFS6 datastore are they from the same storage array/backend device or not.
Also have you tried cloning the vm from VMFS5 to VMFS6 as a troubleshooting step - test wise?
since multiple vms are affected then it would be best to open case with GSS to work on this as this will require input from both storage vendor and VM Guest OS vendor.