My FileVault image grew bigger than 1 GB today, so I decided that it needed to be reset since a 300 MB account should not grow into a 1 GB FV image. I deactivated FV and reactivated it, and the FV image grew to a reasonable 400 MB. Apparently, every time OS X crashes and needs a reboot, FV forgets to shrink the size of the image. After each forced reboot, the image grows larger until it fills up the hard drive.
The user doesn't see this unless the size of the FV image is checked from root or another account. If you're missing a lot of space, it might be FileVault that's eating it.