It happened with me alos this year . First i was issued two year work permit and I reapplied paper based and got three years . First I called CIC agent and explained him everything that I am eligible for three years work permit and he then sent me a form to correct expiry date on work permit on my email.
here it is>>
Thank you for contacting Citizenship and Immigration Canada. I am pleased to follow up on your request:
Correction of the expiry date on an Immigration Document
If there is an error with the expiry date on your immigration document (e.g., visitor record, work permit, study permit, etc.), you must:
Complete the Application to Change Conditions or Extend Your Stay in Canada;
Include an explanation letter detailing the error; and
Send everything to the Case processing centre in Vegreville, Alberta.
Hope this will help