TM Backs up too much

In Time Machine Preferences, click the "Options..." button and exclude the directory where the VMs are stored and see if that makes a difference (if not we'll need to move onto considering something else). VMs should be backed up separately to using Time Machine. Time Machine doesn't work very well with backing up huge files that are changed regularly (e.g. VMs) and these should be backed up separately. Your VM software might have a feature too that allows you to rollback the VM to a saved state in the case you make a mistake (of course this isn't a replacement for backups as your Mac HDD might die, the VM file could be corrupted etc.).