I had a situation recently where I wanted to delete about 10 Snapshot from a VMWare Fusion VM.

VMWare managed to delete the snapshots from the Snapshots manager window but also gave me the lovely error message:

Unable to clean up deleted files. There is not enough space on the file system for the selected operation


I could see in the Virtual Machine folder that all the snapshot files were still there and taking up all the disk space I was trying to reclaim.

The solution was to create a new snapshot in Snapshot manager and then to delete it.  This re-started the "Cleaning up deleted files..." process which duly went through and cleaned up the old snapshot files.