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Not all capital gains are eligible for the capital gains deduction as discussed in the Canada Revenue Agency (CRA) documentation:
https://www.canada.ca/en/revenue-agency/services/tax/individuals/topics/about-your-tax-return/tax-return/completing-a-tax-return/deductions-credits-expenses/line-254-capital-gains-deduction/what-deduction-limit.html
Publicly traded securities transactions reported on a T5008 would not be eligible for the capital gains deduction. The types of capital gains transactions reported on T5008 are listed in the following CRA link:
https://www.canada.ca/en/revenue-agency/services/forms-publications/publications/t4091/t5008-guide-return-securities-transactions-2016.html#P40_9101
So, TurboTax will not automatically apply the capital gains deduction for publicly traded securities posted to section 3 of the schedule 3 from the T5008 slip, which follows the CRA rules.
Hope this helps