Are you speaking hypothetically or are you having a reoccurring issue with a single employee?
Your written SOP, policy and training records that are signed off are all preventative measures....but you cannot prevent employees from mucking up no matter how hard you try. If you include company policy regarding formal warnings (which are included as a good thing by CFIA) in your policy for the audit to see it should add merit to your overall plan.
Is it a single employee not following policy all the time? are they the only employee who performs that task? Can you rewrite you policy to be in compliance at all times?
And btw, if the employees are being assessed internally for following the procedure, how is it that they are still not performing the task correctly?
Maybe you need a root cause analysis to figure out why a particular step is proving difficult to manage