In Ubuntu 12.04 I was used to run the 'Disk Utility' and choose 'Check Filesystem'; its subtitle showed also 'and repair'. In Ubuntu 16.04 I have only found the 'Disks' utility that looks similarly but has no 'Check Filesystem' option, even for the superuser.
Ubuntu – how to check a filesystem in Ubuntu 16.04
To check the file system on your Ubuntu partition...
sudo fsck -f /
fsckcommand if there were errors
If for some reason you can't do the above...
gpartedand determine which /dev/sdaX is your Ubuntu EXT4 partition
sudo fsck -f /dev/sdaX# replacing X with the number you found earlier