Hyper-V snapshots exist after Shut Down

I know its not going to answer your problem, but I have a few VMWare images that get compacted reasonably regularly, and I've never had the problem you describe.

I'd try again and see if you get the same errors, it's possible it was a 'glitch' (but I guess that still doesn't help if you can't trust the operation any more)

I gathered from the comments to MDMarra's answer that some users need (need or want?) to be able to start and stop VMs. If users do have a valid case for having direct control over a server, such as when they are used for dev work, consider placing those VM's on the users' workstations. Use whatever virtualisation product you like for the job, such as Virtualbox, VMWare Player, Virtual PC, etc.

Your situation screams two fundamental problems:

1. The rule of least privileges should always be applied.
2. Never allow users to access or do anything for which you might be held accountable. It's easy enough to make mistakes. You don't need users making them for you.