This may be a problem with Disk Utility on your boot drive. Try rebooting to the Recovery HD and using Disk Utility on that partition (it should appear in the OS X Tools menu). You might also try running a disk verification and repair to ensure the filesystem and partition structure are intact.
Alternatively you can also bypass the disk utility application by using the Terminal to erase free space, which can be done with the following command:
sudo diskutil secureErase freespace 0 disk0s2
Note that while the device "disk0s2" is commonly the boot drive for systems with a single hard drive, this may be different for you system. Check the device by opening Disk Utility and getting information on your boot volume, and you should see the proper device name listed as "device identifier."