The answer is "for not much longer". It will be hard to argue that the CRA should be lenient in regards to any harmonized sales tax ("HST") implementaion errors --- but, I can gurantee you that every lawyer who practices in this error will try. We have a number of good reasons to request leniency.
That is not the point of this posting. The point I am trying to make is that if you are not sure that your implementation efforts are correct, it would be prudent to conduct an internal audit and check your GST/HST systems. Finding errors before the one-year anniversary of HST in Ontario and British Columbia is better than not asking the question at all. Do not be afraid of what you might find -- be more concerned about not finding the errors and being audited by an unforgiving CRA auditor. The CRA may be lenient if you conduct an internal audit and adjust systems before the one year anniversary. They may see this as a sign of compliance and of acting as a "good" suppler/purchaser/consumer.
What I can tell you is that if you undertake an internal audit and find the errors and fix the system errors, you will have good argument that you deserve lenient treatment. Mom used to say "actions speak louder than words".