Perhaps the item most often overlooked by Canadians taxpayers undertaking a commercial activity (such as a business or real estate investment) or non-profit/charitable activity is the GST / HST. The number and complexity of rules that Canadian taxpayers are expected to comply with regularly catches people by surprise.
These problems can be even more significant because many Canadians consider the rules not to be intuitive/make sense, the cost of non-compliance can be staggering, CRA generally provides no leniency / relief in respect of non-compliance, geographic factors can greatly complicate the rules, and the CRA (recognizing their potential to generate revenues) is greatly increasing their audit activity in this area.
Regular discussion with a GST / HST expert should be maintained throughout the life of your business or commercial undertaking. In particular, guidance should be sought at the start, upon any significant changes, and at the end.