Entered US Aug. 27th 2016 and today is the 90 day mark. I will leave the US in time but will be in Canada for 12 hrs into the 91st day. How will this affect my ESTA status and future plans for I-129F visa?
Although stays in Canada famously do not reset the Visa Waiver Program 90 day clock*, that does not mean that stays in Canada after you have exited the US for the last time in a trip are added to your stay. US CBP does not care how long you stay in Canada. The clock does not reset when you make a short Canada visit and return to the US solely because they do not want people to do a 'visa run' to Canada for a few days and then claim a new 90 day period of time in the US.
As long as you leave the US within the time limit you will be fine for this trip, your next VWP visit, and any visas you decide to apply for.
*For the record, ESTA is nothing to do with the 90 day rule. The rule is about the Visa Waiver Program (VWP), which is what allows you to visit the US without a visa. ESTA is simply a form that gives you permission to get on a plane to the US, although many people wrongly use 'ESTA" when they mean the VWP.