Time machine is not reliable for backing up virtual machines. You're likely experiencing the results of a corrupted backup.
The best option is to try to find a time when you know the machine wasn't running, and had been shut down (not suspended) and restore back to that point in time. You might get lucky!
I know it's too late now, but for the future, it's best to just disable time machine for the virtual machine (it's a waste of space) and make manual backups (with the machine shut down) using finder or a program like Carbon Copy Cloner or SuperDuper.