Yes, one such circumstance where the CRA can refuse to issue your refund is when the taxable income for a tax year is reported after 3 years of the reporting period. For example, if the tax return for the 2008 year is filed on September 2013, the CRA can refuse to issue that refund because it has been more than 3 years from the due date of the 2008 return (which would have been April 2009).
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