Yes, if you are a taxpayer reporting Self-Employed income on a Statement of Business Activities form (most commonly the T2125), TurboTax will calculate the CPP Contributions payable on any Net Self-Employed Income over $3,500.
See this TurboTax tip: CPP and EI Considerations For Self-Employed Canadians
If you are an employee and receiving income on T4 tax slips, your CPP is calculated based on the entries you make from the T4 slip itself. If it is calculated that you have "overpaid CPP or EI premiums", you will be refunded the amounts you have overpaid.
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