Citizenship doesn't matter for tax purposes, only your residency status. You can be a Canadian citizen but not a resident, or citizen of a different country, but still be considered a resident for tax purposes.
One of the first questions that TurboTax asks is if you are a resident, deemed resident or non-resident, so you would want to check your return to see what you answered. What you enter for residency status in TurboTax just tells the software what forms you need for your return. It doesn't change what the CRA believes your residency status is. If you believe the CRA has incorrectly labeled you a non-resident, then you would need to contact them to see how you can resolve that matter.
If you are in Canada or the United States, you can call the CRA at 1-800-959-8281. If you are elsewhere, you can call 613-940-8495. This page has more ways to contact the CRA: Contact the Canada Revenue Agency
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