I got a issue like this on my previous thinkpad. If i remember good, i made it fully stop HW side adding a setting to grub :
Inside /etc/default/grub change this setting :
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
to
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash acpi=force"
you can edit the file with nano that is simple to use :
sudo nano /etc/default/grub
Next do a grub update with this command :
sudo update-grub
Next reboot and once back try shutdown again.
Edit : I saw also that some guys are using this setting at the same place :
GRUB_CMDLINE_LINUX_DEFAULT="apm=power_off"
You can give it a try but if the first one is not working - acpi=force
The good think now is how much you will learn troubleshooting your problem and how good time you will spend on it 
Let's give a chance to this settings otherwise we will continue digging !