If I watch the entire Scan process at one point it does return sucessful and I can click on the completed results and perform a patch. If I just scan and come back some time later that's were the results show there was a failure.
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Some things that might be worth checking when you get the scan error that you mentioned:
-Make sure to hit the "refresh server" button under the hosted virtual machines tab of your group before running the scan. If the last known power state of the VM is different from its actual current state when you run the scan it will fail because Protect attempts to scan the VM in a different manner depending if it's offline or online.
-Make sure the VM is not in a power state such as "paused" or "suspended".
-Make sure the VM has not been vmotioned to a different host. The first thing mentioned above to refresh the servers in Protect should clear this up if it has.
-I have seen manually changing the power state of the VM help for this error as well. Possibly power off/on the VM to see if it helps clear up the problem.
I hope this helps!