You don't say what command you're using, so do it this way...
To check the file system on your Ubuntu partition...
- boot to the GRUB menu
- choose Advanced Options
- choose Recovery mode
- choose Root access
- at the # prompt, type
sudo fsck -f /
- repeat the
fsck command if there were errors
If for some reason you can't do the above...
- boot to a Ubuntu Live DVD/USB
gparted and determine which /dev/sdaX is your Ubuntu EXT4 partition
- open a
sudo fsck -f /dev/sda4 # replacing 4 with the number you found earlier
- repeat the fsck command if there were errors