My wife's application for PR is pending with CIC. She is here with me in Canada on TRV (multiple entry). She first entered Canada on 01 March 2015 so she could have stayed until 31 August 2015 (max 6 moths at a stretch). As she has US visa too, we went to NYC last month and she re-entered Canada on 20 June 2015. Can she now stay here for another 6 months from the last entry date of 20 June 2015 with applying for extension to CIC?
It only matters what CBSA did. What US Border Security did is irrelevant.
You need to assume she was readmitted based on her original visit (rather than admitted as a new visitor) which means her visit still expires in August 2015. She will need to apply for an extension if she wishes to remain in Canada past that date.