Before I went for my frst scan my midwife told me that I would be 12 weeks and 1 day on the day of my scan that was calculated from the first day of my last period, my scan was on 28th January, 2011 but the scan person told me that I was actually 13 weeks pregnant instead so now I'm confused as to when my conception date was because I had my period on 4th November, 2010 as usual but it only lasted 3 days.

You can have a light period while you are pregnant, some doctors call this implantation bleeding. It can happen when the fertilized egg attachs itself to the uterine wall.
Also scans can vary due dates by a few days. I have had my due date change a few times based on the babies growth. You probably conceived a day before or after Nov.17/10
There are a lot of really good baby/pregnancy sites that help track your dates babygaga.com is a good one.