There is a bug when you enter a principal residence sale where you only used it as your principal residence "some of the time".

[ePeggyH]

To see if this bug affects you cross-check the calculated amount of Taxable Capital Gains on the Principal Residence details shown after entering the details of your Principal Residence sale against the figure carried forward to the tax details summary on Capital Gains line. It should be the same i.e. 50% of the actual capital gain. In my case (and perhaps yours) it was reduced by 50% a second time.  

I used "Turbo Live" and checked with one of their experts who agreed this was a bug and the workaround was to enter it as an investment capital gain and not to complete the Principal Residence declaration (which is what the CRA states in their info circular that you should do).  I also advised them that anyone who uses the Principal Residence form to calculate their capital gain on the sale of their Principal Residence, in the case of it being their principal residence "some of the time",  will be only claiming 25% of the capital gain as taxable and this will be flagged by CRA and a much larger tax bill will be owed.

[TurboTaxGinette]

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